├── report ├── calls.rst ├── depths.rst ├── freq.rst ├── snpeff.rst ├── vcf.rst ├── sv.rst ├── snv.rst ├── multiqc.rst └── workflow.rst ├── scripts ├── str │ ├── __init__.py │ ├── core │ │ └── __init__.py │ └── str_helper.sh ├── common.py ├── SVRecords │ └── __init__.py └── annotate-caller.sh ├── samples.tsv ├── wrappers ├── bwa │ ├── aln │ │ ├── test │ │ │ ├── genome.amb │ │ │ ├── genome.fasta │ │ │ ├── genome.ann │ │ │ ├── reads │ │ │ │ ├── a.1.fastq │ │ │ │ └── a.2.fastq │ │ │ ├── genome.sa │ │ │ ├── genome.bwt │ │ │ ├── genome.pac │ │ │ └── Snakefile │ │ ├── meta.yaml │ │ ├── environment.yaml │ │ └── wrapper.py │ ├── mem │ │ ├── test │ │ │ ├── genome.amb │ │ │ ├── genome.fasta │ │ │ ├── genome.ann │ │ │ ├── reads │ │ │ │ ├── a.1.fastq │ │ │ │ └── a.2.fastq │ │ │ ├── genome.sa │ │ │ ├── genome.bwt │ │ │ ├── genome.pac │ │ │ ├── Snakefile │ │ │ ├── Snakefile_picard │ │ │ └── Snakefile_samtools │ │ ├── environment.yaml │ │ └── meta.yaml │ ├── sampe │ │ ├── test │ │ │ ├── genome.amb │ │ │ ├── genome.fasta │ │ │ ├── genome.ann │ │ │ ├── reads │ │ │ │ ├── a.1.fastq │ │ │ │ └── a.2.fastq │ │ │ ├── genome.sa │ │ │ ├── genome.bwt │ │ │ ├── genome.pac │ │ │ ├── sai │ │ │ │ ├── a.1.sai │ │ │ │ └── a.2.sai │ │ │ ├── Snakefile │ │ │ ├── Snakefile_picard │ │ │ └── Snakefile_samtools │ │ ├── meta.yaml │ │ └── environment.yaml │ ├── samse │ │ ├── test │ │ │ ├── genome.amb │ │ │ ├── genome.fasta │ │ │ ├── genome.ann │ │ │ ├── reads │ │ │ │ └── a.1.fastq │ │ │ ├── genome.sa │ │ │ ├── genome.bwt │ │ │ ├── genome.pac │ │ │ ├── sai │ │ │ │ └── a.1.sai │ │ │ ├── Snakefile │ │ │ ├── Snakefile_picard │ │ │ └── Snakefile_samtools │ │ ├── meta.yaml │ │ └── environment.yaml │ ├── mem-samblaster │ │ ├── test │ │ │ ├── genome.amb │ │ │ ├── genome.fasta │ │ │ ├── genome.ann │ │ │ ├── reads │ │ │ │ ├── a.1.fastq │ │ │ │ └── a.2.fastq │ │ │ ├── genome.sa │ │ │ ├── genome.bwt │ │ │ ├── genome.pac │ │ │ └── Snakefile │ │ ├── environment.yaml │ │ └── meta.yaml │ └── index │ │ ├── test │ │ ├── genome.fasta │ │ └── Snakefile │ │ ├── meta.yaml │ │ └── environment.yaml ├── bcftools │ ├── reheader │ │ ├── test │ │ │ ├── samples.tsv │ │ │ ├── a.bcf │ │ │ ├── Snakefile │ │ │ └── header.txt │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── concat │ │ ├── test │ │ │ ├── a.bcf │ │ │ ├── b.bcf │ │ │ └── Snakefile │ │ ├── environment.yaml │ │ └── meta.yaml │ ├── index │ │ ├── test │ │ │ ├── a.bcf │ │ │ ├── a.bcf.csi │ │ │ └── Snakefile │ │ ├── meta.yaml │ │ ├── environment.yaml │ │ └── wrapper.py │ ├── merge │ │ ├── test │ │ │ ├── a.bcf │ │ │ ├── b.bcf │ │ │ ├── a.bcf.csi │ │ │ ├── b.bcf.csi │ │ │ └── Snakefile │ │ ├── meta.yaml │ │ ├── environment.yaml │ │ └── wrapper.py │ ├── call │ │ ├── meta.yaml │ │ └── environment.yaml │ ├── isec │ │ ├── environment.yaml │ │ └── wrapper.py │ ├── norm │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ ├── test │ │ │ └── Snakefile │ │ └── wrapper.py │ ├── view │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ └── test │ │ │ └── Snakefile │ ├── annotate │ │ ├── environment.yaml │ │ └── wrapper.py │ ├── filter │ │ └── environment.yaml │ └── stats │ │ ├── environment.yaml │ │ └── wrapper.py ├── bedtools │ ├── intersect │ │ ├── test │ │ │ ├── A.bed │ │ │ ├── B.bed │ │ │ └── Snakefile │ │ ├── meta.yaml │ │ ├── environment.yaml │ │ └── wrapper.py │ ├── slop │ │ ├── test │ │ │ ├── genome.txt │ │ │ ├── A.bed │ │ │ └── Snakefile │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── merge │ │ ├── test │ │ │ ├── A.bed │ │ │ └── Snakefile │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── bamtofastq │ │ └── environment.yaml │ └── coveragebed │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ ├── test │ │ └── Snakefile │ │ └── wrapper.py ├── platypus │ ├── test │ │ ├── genome.fasta.fai │ │ ├── mapped │ │ │ ├── a.bam.bai │ │ │ └── a.bam │ │ ├── regions.bed │ │ ├── genome.fasta │ │ └── Snakefile │ ├── environment.yaml │ └── meta.yaml ├── samtools │ ├── depth │ │ ├── test │ │ │ ├── regionToCalcDepth.bed │ │ │ ├── mapped │ │ │ │ ├── A.bam │ │ │ │ └── B.bam │ │ │ └── Snakefile │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── mpileup │ │ ├── test │ │ │ ├── mapped │ │ │ │ ├── a.bam.bai │ │ │ │ └── a.bam │ │ │ ├── genome.fasta.fai │ │ │ ├── genome.fasta │ │ │ └── Snakefile │ │ ├── meta.yaml │ │ └── environment.yaml │ ├── faidx │ │ ├── environment.yaml │ │ ├── test │ │ │ ├── genome.fa │ │ │ └── Snakefile │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── index │ │ ├── environment.yaml │ │ ├── test │ │ │ ├── mapped │ │ │ │ └── a.sorted.bam │ │ │ └── Snakefile │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── markdup │ │ └── environment.yaml │ ├── merge │ │ ├── environment.yaml │ │ ├── test │ │ │ ├── mapped │ │ │ │ ├── A.bam │ │ │ │ └── B.bam │ │ │ └── Snakefile │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── sort │ │ ├── environment.yaml │ │ ├── test │ │ │ ├── mapped │ │ │ │ ├── a.bam │ │ │ │ └── a.bam.bai │ │ │ └── Snakefile │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── stats │ │ ├── environment.yaml │ │ ├── test │ │ │ ├── mapped │ │ │ │ ├── a.bam │ │ │ │ └── a.bam.bai │ │ │ └── Snakefile │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── view │ │ ├── environment.yaml │ │ ├── wrapper.py │ │ └── test │ │ │ ├── Snakefile │ │ │ └── a.sam │ ├── fixmate │ │ ├── test │ │ │ ├── mapped │ │ │ │ └── a.bam │ │ │ └── Snakefile │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── flagstat │ │ ├── environment.yaml │ │ ├── test │ │ │ ├── mapped │ │ │ │ └── a.bam │ │ │ └── Snakefile │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── idxstats │ │ ├── environment.yaml │ │ ├── test │ │ │ ├── mapped │ │ │ │ ├── a.sorted.bam │ │ │ │ └── a.sorted.bam.bai │ │ │ └── Snakefile │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── bam2fq │ │ ├── separate │ │ │ ├── environment.yaml │ │ │ ├── test │ │ │ │ ├── mapped │ │ │ │ │ └── a.bam │ │ │ │ ├── reads │ │ │ │ │ ├── a.1.fq │ │ │ │ │ └── a.2.fq │ │ │ │ └── Snakefile │ │ │ └── meta.yaml │ │ └── interleaved │ │ │ ├── environment.yaml │ │ │ ├── test │ │ │ ├── mapped │ │ │ │ └── a.bam │ │ │ ├── Snakefile │ │ │ └── reads │ │ │ │ └── a.fq │ │ │ ├── meta.yaml │ │ │ └── wrapper.py │ └── fastq │ │ └── environment.yaml ├── gatk │ ├── mutect │ │ ├── test │ │ │ ├── mapped │ │ │ │ ├── a.bam.bai │ │ │ │ └── a.bam │ │ │ ├── genome │ │ │ │ ├── genome.fasta.fai │ │ │ │ ├── genome.fasta │ │ │ │ └── genome.dict │ │ │ └── Snakefile │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── haplotypecaller │ │ ├── test │ │ │ ├── mapped │ │ │ │ ├── a.bam.bai │ │ │ │ └── a.bam │ │ │ ├── genome.fasta.fai │ │ │ ├── genome.fasta │ │ │ ├── genome.dict │ │ │ └── Snakefile │ │ ├── environment.yaml │ │ └── meta.yaml │ ├── combinegvcfs │ │ ├── test │ │ │ ├── genome.fasta.fai │ │ │ ├── genome.fasta │ │ │ ├── genome.dict │ │ │ └── Snakefile │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── variantrecalibrator │ │ ├── test │ │ │ └── genome.fasta │ │ ├── environment.yaml │ │ └── meta.yaml │ ├── baserecalibrator │ │ ├── test │ │ │ ├── genome.fasta.fai │ │ │ ├── dbsnp.vcf.gz │ │ │ ├── mapped │ │ │ │ └── a.bam │ │ │ ├── dbsnp.vcf.gz.tbi │ │ │ ├── genome.fasta │ │ │ ├── genome.dict │ │ │ └── Snakefile │ │ ├── environment.yaml │ │ └── meta.yaml │ ├── genotypegvcfs │ │ ├── test │ │ │ ├── genome.fasta.fai │ │ │ ├── genome.fasta │ │ │ ├── genome.dict │ │ │ └── Snakefile │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── selectvariants │ │ ├── test │ │ │ ├── genome.fasta.fai │ │ │ ├── genome.fasta │ │ │ ├── genome.dict │ │ │ └── Snakefile │ │ ├── environment.yaml │ │ ├── wrapper.py │ │ └── meta.yaml │ ├── splitncigarreads │ │ ├── test │ │ │ ├── genome.fasta.fai │ │ │ ├── mapped │ │ │ │ └── a.bam │ │ │ ├── genome.fasta │ │ │ ├── genome.dict │ │ │ └── Snakefile │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── variantfiltration │ │ ├── test │ │ │ ├── genome.fasta.fai │ │ │ ├── genome.fasta │ │ │ ├── genome.dict │ │ │ └── Snakefile │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ └── wrapper.py │ └── filtermutectcalls │ │ ├── environment.yaml │ │ └── wrapper.py ├── fastqc │ ├── test │ │ ├── reads │ │ │ └── a.fastq │ │ └── Snakefile │ ├── environment.yaml │ └── meta.yaml ├── gatk3 │ ├── haplotypecaller │ │ ├── test │ │ │ ├── mapped │ │ │ │ ├── a.bam.bai │ │ │ │ └── a.bam │ │ │ ├── genome.fasta.fai │ │ │ ├── genome.fasta │ │ │ ├── genome.dict │ │ │ └── Snakefile │ │ └── environment.yaml │ ├── printreads │ │ ├── environment.yaml │ │ ├── test │ │ │ ├── README.md │ │ │ └── Snakefile │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── baserecalibrator │ │ ├── environment.yaml │ │ ├── test │ │ │ ├── README.md │ │ │ └── Snakefile │ │ └── meta.yaml │ ├── indelrealigner │ │ ├── environment.yaml │ │ └── test │ │ │ ├── README.md │ │ │ └── Snakefile │ └── realignertargetcreator │ │ ├── environment.yaml │ │ ├── test │ │ ├── README.md │ │ └── Snakefile │ │ └── meta.yaml ├── picard │ ├── collecthsmetrics │ │ ├── test │ │ │ ├── genome.fasta.fai │ │ │ ├── genome.fasta │ │ │ ├── genome.dict │ │ │ ├── mapped │ │ │ │ └── a.bam │ │ │ ├── regions.intervals │ │ │ └── Snakefile │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── collectalignmentsummarymetrics │ │ ├── test │ │ │ ├── genome.fasta.fai │ │ │ ├── genome.fasta │ │ │ ├── mapped │ │ │ │ └── a.bam │ │ │ └── Snakefile │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── sortsam │ │ ├── test │ │ │ ├── mapped │ │ │ │ └── a.bam │ │ │ └── Snakefile │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── revertsam │ │ ├── test │ │ │ ├── mapped │ │ │ │ └── a.bam │ │ │ └── Snakefile │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── samtofastq │ │ ├── test │ │ │ ├── mapped │ │ │ │ └── a.bam │ │ │ └── Snakefile │ │ ├── environment.yaml │ │ └── meta.yaml │ ├── mergesamfiles │ │ ├── test │ │ │ ├── mapped │ │ │ │ ├── a.bam │ │ │ │ └── b.bam │ │ │ └── Snakefile │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── gathervcfs │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── mergevcfs │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ ├── test │ │ │ └── Snakefile │ │ └── wrapper.py │ ├── markduplicates │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ └── test │ │ │ └── Snakefile │ ├── addorreplacereadgroups │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ ├── test │ │ │ └── Snakefile │ │ └── wrapper.py │ ├── collectinsertsizemetrics │ │ ├── test │ │ │ ├── mapped │ │ │ │ └── a.bam │ │ │ └── Snakefile │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ └── wrapper.py │ ├── collecttargetedpcrmetrics │ │ ├── environment.yaml │ │ ├── test │ │ │ ├── mapped │ │ │ │ └── a.bam │ │ │ ├── target.list │ │ │ ├── amplicon.list │ │ │ └── Snakefile │ │ ├── meta.yaml │ │ └── wrapper.py │ └── createsequencedictionary │ │ ├── environment.yaml │ │ ├── test │ │ ├── genome.fasta │ │ └── Snakefile │ │ ├── meta.yaml │ │ └── wrapper.py ├── igv-reports │ ├── test │ │ ├── minigenome.fa │ │ ├── variants.vcf │ │ ├── alignments.bam │ │ ├── alignments.bam.bai │ │ ├── minigenome.fa.fai │ │ └── Snakefile │ ├── environment.yaml │ ├── meta.yaml │ └── wrapper.py ├── metasv │ ├── environment.yaml │ └── wrapper.py ├── mosdepth │ ├── environment.yaml │ └── wrapper.py ├── tabix │ ├── test │ │ ├── test.vcf.gz │ │ └── Snakefile │ ├── environment.yaml │ ├── meta.yaml │ └── wrapper.py ├── wham │ ├── environment.yaml │ └── wrapper.py ├── reference │ ├── ensembl-sequence │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ └── test │ │ │ └── Snakefile │ ├── ensembl-annotation │ │ ├── environment.yaml │ │ ├── meta.yaml │ │ └── test │ │ │ └── Snakefile │ └── ensembl-variation │ │ ├── environment.yaml │ │ ├── test │ │ ├── refs │ │ │ ├── variation.vcf.gz │ │ │ ├── variation.vcf.gz.tbi │ │ │ └── genome.fasta.fai │ │ ├── with_fai.smk │ │ └── Snakefile │ │ └── meta.yaml ├── vcflib │ ├── environment.yaml │ └── wrapper.py ├── vep │ ├── meta.yaml │ ├── environment.yaml │ └── test │ │ ├── fake_KJ660346.vcf │ │ └── Snakefile ├── vcfanno │ ├── environment.yaml │ ├── meta.yaml │ └── test │ │ ├── fake_KJ660346.vcf │ │ └── Snakefile ├── vcf2db │ ├── meta.yaml │ ├── environment.yaml │ └── test │ │ ├── fake_KJ660346.vcf │ │ └── Snakefile ├── vcftools │ └── filter │ │ ├── meta.yaml │ │ ├── environment.yaml │ │ ├── test │ │ └── Snakefile │ │ └── wrapper.py ├── vt │ ├── environment.yaml │ ├── meta.yaml │ ├── test │ │ ├── Snakefile │ │ └── fake_KJ660346.vcf │ └── wrapper.py ├── EH │ ├── environment.yaml │ └── wrapper.py ├── EHdn │ ├── environment.yaml │ └── wrapper.py ├── qualimap │ ├── environment.yaml │ └── meta.yaml ├── snpeff │ ├── environment.yaml │ ├── meta.yaml │ ├── test │ │ ├── fake_KJ660346.vcf │ │ ├── Snakefile_nostats │ │ └── Snakefile │ └── wrapper.py ├── manta │ ├── environment.yaml │ └── wrapper.py ├── verifybamid2 │ ├── environment.yaml │ ├── meta.yaml │ └── wrapper.py ├── peddy │ ├── environment.yaml │ └── wrapper.py ├── rtg-tools │ ├── vcfeval │ │ └── environment.yaml │ └── vcfsubset │ │ ├── environment.yaml │ │ └── wrapper.py ├── freebayes │ ├── meta.yaml │ └── environment.yaml ├── samblaster │ ├── environment.yaml │ └── wrapper.py ├── multiqc │ ├── environment.yaml │ ├── meta.yaml │ ├── test │ │ └── Snakefile │ └── wrapper.py ├── smoove │ ├── environment.yaml │ └── wrapper.py ├── report_upload │ ├── post_report │ │ └── environment.yaml │ └── PT_identifier │ │ └── environment.yaml ├── fastq_screen │ ├── environment.yaml │ └── test │ │ └── Snakefile └── mity │ ├── call │ ├── environment.yaml │ └── wrapper.py │ ├── normalise │ ├── environment.yaml │ └── wrapper.py │ └── report │ └── environment.yaml ├── crg2logolarge.png ├── pbs_profile ├── pbs_jobscript.sh ├── config.yaml.save ├── config.yaml └── pbs_status.py ├── slurm_profile ├── slurm-jobscript.sh ├── settings.json └── config.yaml ├── envs ├── rtg.yaml ├── rbt.yaml ├── samtools.yaml ├── ehdn.yaml ├── stats.yaml ├── coverage.yaml ├── hpo_to_panel.yaml ├── eh-report.yaml ├── common.yaml ├── melt.yaml ├── ehdn_outlier.yaml ├── mt_report.yaml ├── ehdn-dbscan.yaml ├── crg.yaml ├── svscore.yaml ├── cre.yaml └── ehdn-report.yaml ├── units.tsv ├── rules ├── multiqc_config.yaml ├── snpeff.smk ├── validation.smk └── stats.smk ├── schemas └── samples.schema.yaml ├── benchmark_cheo_ri.tsv ├── benchmark_hpf.tsv ├── sample_info.tsv ├── get_dependency.sh ├── dnaseq.pbs ├── dnaseq_slurm_hpf.sh ├── validation.pbs ├── utils ├── wgs_gene_coverage │ └── README.md └── check_dup_rate.sh ├── dnaseq_slurm_cheo_ri.sh ├── programs.03-18-2021.txt └── dnaseq_cluster.pbs /report/calls.rst: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /report/depths.rst: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /report/freq.rst: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /report/snpeff.rst: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /report/vcf.rst: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /scripts/str/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /scripts/str/core/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /samples.tsv: -------------------------------------------------------------------------------- 1 | sample 2 | NA12878 3 | -------------------------------------------------------------------------------- /wrappers/bwa/aln/test/genome.amb: -------------------------------------------------------------------------------- 1 | 20 1 0 2 | -------------------------------------------------------------------------------- /wrappers/bwa/mem/test/genome.amb: -------------------------------------------------------------------------------- 1 | 20 1 0 2 | -------------------------------------------------------------------------------- /wrappers/bwa/sampe/test/genome.amb: -------------------------------------------------------------------------------- 1 | 20 1 0 2 | -------------------------------------------------------------------------------- /wrappers/bwa/samse/test/genome.amb: -------------------------------------------------------------------------------- 1 | 20 1 0 2 | -------------------------------------------------------------------------------- /report/sv.rst: -------------------------------------------------------------------------------- 1 | SV results: {{snakemake.output}} 2 | -------------------------------------------------------------------------------- /wrappers/bcftools/reheader/test/samples.tsv: -------------------------------------------------------------------------------- 1 | SAMPLE_A 2 | -------------------------------------------------------------------------------- /wrappers/bwa/mem-samblaster/test/genome.amb: -------------------------------------------------------------------------------- 1 | 20 1 0 2 | -------------------------------------------------------------------------------- /report/snv.rst: -------------------------------------------------------------------------------- 1 | SNV Results {{ snakemake.wildcards.name }} 2 | -------------------------------------------------------------------------------- /wrappers/bedtools/intersect/test/A.bed: -------------------------------------------------------------------------------- 1 | 1 1 20 2 | 2 15 30 3 | -------------------------------------------------------------------------------- /wrappers/bedtools/slop/test/genome.txt: -------------------------------------------------------------------------------- 1 | 1 1000 2 | 2 1000 3 | -------------------------------------------------------------------------------- /wrappers/platypus/test/genome.fasta.fai: -------------------------------------------------------------------------------- 1 | Sheila 20 8 20 21 2 | -------------------------------------------------------------------------------- /wrappers/platypus/test/mapped/a.bam.bai: -------------------------------------------------------------------------------- 1 | BAI -------------------------------------------------------------------------------- /wrappers/platypus/test/regions.bed: -------------------------------------------------------------------------------- 1 | Sheila 0 2 2 | Sheila 6 9 -------------------------------------------------------------------------------- /wrappers/samtools/depth/test/regionToCalcDepth.bed: -------------------------------------------------------------------------------- 1 | xx 0 500 2 | -------------------------------------------------------------------------------- /report/multiqc.rst: -------------------------------------------------------------------------------- 1 | Reports from MultiQC {{snakemake.output}} 2 | -------------------------------------------------------------------------------- /scripts/common.py: -------------------------------------------------------------------------------- 1 | import matplotlib 2 | matplotlib.use("agg") 3 | -------------------------------------------------------------------------------- /wrappers/bwa/index/test/genome.fasta: -------------------------------------------------------------------------------- 1 | >Sheila 2 | GCTAGCTCAGAAAAAAAAAA -------------------------------------------------------------------------------- /wrappers/gatk/mutect/test/mapped/a.bam.bai: -------------------------------------------------------------------------------- 1 | BAI -------------------------------------------------------------------------------- /wrappers/bwa/aln/test/genome.fasta: -------------------------------------------------------------------------------- 1 | >Sheila 2 | GCTAGCTCAGAAAAAAAAAA 3 | -------------------------------------------------------------------------------- /wrappers/bwa/mem/test/genome.fasta: -------------------------------------------------------------------------------- 1 | >Sheila 2 | GCTAGCTCAGAAAAAAAAAA 3 | -------------------------------------------------------------------------------- /wrappers/bwa/sampe/test/genome.fasta: -------------------------------------------------------------------------------- 1 | >Sheila 2 | GCTAGCTCAGAAAAAAAAAA 3 | -------------------------------------------------------------------------------- /wrappers/bwa/samse/test/genome.fasta: -------------------------------------------------------------------------------- 1 | >Sheila 2 | GCTAGCTCAGAAAAAAAAAA 3 | -------------------------------------------------------------------------------- /wrappers/fastqc/test/reads/a.fastq: -------------------------------------------------------------------------------- 1 | @1 2 | ACGGCAT 3 | + 4 | !!!!!!! 5 | -------------------------------------------------------------------------------- /wrappers/platypus/test/genome.fasta: -------------------------------------------------------------------------------- 1 | >Sheila 2 | GCTAGCTCAGAAAAAAAAAA 3 | -------------------------------------------------------------------------------- /wrappers/samtools/mpileup/test/mapped/a.bam.bai: -------------------------------------------------------------------------------- 1 | BAI -------------------------------------------------------------------------------- /wrappers/bedtools/intersect/test/B.bed: -------------------------------------------------------------------------------- 1 | 1 10 40 2 | 1 100 150 3 | 2 1 20 4 | -------------------------------------------------------------------------------- /wrappers/bwa/aln/test/genome.ann: -------------------------------------------------------------------------------- 1 | 20 1 11 2 | 0 Sheila (null) 3 | 0 20 0 4 | -------------------------------------------------------------------------------- /wrappers/bwa/aln/test/reads/a.1.fastq: -------------------------------------------------------------------------------- 1 | @1 2 | ACGGCAT 3 | + 4 | !!!!!!! 5 | -------------------------------------------------------------------------------- /wrappers/bwa/aln/test/reads/a.2.fastq: -------------------------------------------------------------------------------- 1 | @1 2 | ACGGCAT 3 | + 4 | !!!!!!! 5 | -------------------------------------------------------------------------------- /wrappers/bwa/mem/test/genome.ann: -------------------------------------------------------------------------------- 1 | 20 1 11 2 | 0 Sheila (null) 3 | 0 20 0 4 | -------------------------------------------------------------------------------- /wrappers/bwa/mem/test/reads/a.1.fastq: -------------------------------------------------------------------------------- 1 | @1 2 | ACGGCAT 3 | + 4 | !!!!!!! 5 | -------------------------------------------------------------------------------- /wrappers/bwa/mem/test/reads/a.2.fastq: -------------------------------------------------------------------------------- 1 | @1 2 | ACGGCAT 3 | + 4 | !!!!!!! 5 | -------------------------------------------------------------------------------- /wrappers/bwa/sampe/test/genome.ann: -------------------------------------------------------------------------------- 1 | 20 1 11 2 | 0 Sheila (null) 3 | 0 20 0 4 | -------------------------------------------------------------------------------- /wrappers/bwa/sampe/test/reads/a.1.fastq: -------------------------------------------------------------------------------- 1 | @1 2 | ACGGCAT 3 | + 4 | !!!!!!! 5 | -------------------------------------------------------------------------------- /wrappers/bwa/sampe/test/reads/a.2.fastq: -------------------------------------------------------------------------------- 1 | @1 2 | ACGGCAT 3 | + 4 | !!!!!!! 5 | -------------------------------------------------------------------------------- /wrappers/bwa/samse/test/genome.ann: -------------------------------------------------------------------------------- 1 | 20 1 11 2 | 0 Sheila (null) 3 | 0 20 0 4 | -------------------------------------------------------------------------------- /wrappers/bwa/samse/test/reads/a.1.fastq: -------------------------------------------------------------------------------- 1 | @1 2 | ACGGCAT 3 | + 4 | !!!!!!! 5 | -------------------------------------------------------------------------------- /wrappers/gatk/haplotypecaller/test/mapped/a.bam.bai: -------------------------------------------------------------------------------- 1 | BAI -------------------------------------------------------------------------------- /wrappers/gatk3/haplotypecaller/test/mapped/a.bam.bai: -------------------------------------------------------------------------------- 1 | BAI -------------------------------------------------------------------------------- /wrappers/picard/collecthsmetrics/test/genome.fasta.fai: -------------------------------------------------------------------------------- 1 | Sheila 20 8 20 21 2 | -------------------------------------------------------------------------------- /wrappers/bwa/mem-samblaster/test/genome.fasta: -------------------------------------------------------------------------------- 1 | >Sheila 2 | GCTAGCTCAGAAAAAAAAAA 3 | -------------------------------------------------------------------------------- /wrappers/igv-reports/test/minigenome.fa: -------------------------------------------------------------------------------- 1 | upstream/test/data/minigenome/minigenome.fa -------------------------------------------------------------------------------- /wrappers/igv-reports/test/variants.vcf: -------------------------------------------------------------------------------- 1 | upstream/test/data/minigenome/variants.vcf -------------------------------------------------------------------------------- /crg2logolarge.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ccmbioinfo/crg2/HEAD/crg2logolarge.png -------------------------------------------------------------------------------- /wrappers/bwa/mem-samblaster/test/genome.ann: -------------------------------------------------------------------------------- 1 | 20 1 11 2 | 0 Sheila (null) 3 | 0 20 0 4 | -------------------------------------------------------------------------------- /wrappers/bwa/mem-samblaster/test/reads/a.1.fastq: -------------------------------------------------------------------------------- 1 | @1 2 | ACGGCAT 3 | + 4 | !!!!!!! 5 | -------------------------------------------------------------------------------- /wrappers/bwa/mem-samblaster/test/reads/a.2.fastq: -------------------------------------------------------------------------------- 1 | @1 2 | ACGGCAT 3 | + 4 | !!!!!!! 5 | -------------------------------------------------------------------------------- /wrappers/gatk/combinegvcfs/test/genome.fasta.fai: -------------------------------------------------------------------------------- 1 | ref 45 5 45 46 2 | ref2 40 57 40 41 3 | -------------------------------------------------------------------------------- /wrappers/gatk/variantrecalibrator/test/genome.fasta: -------------------------------------------------------------------------------- 1 | >Sheila 2 | GCTAGCTCAGAAAAAAAAAA 3 | -------------------------------------------------------------------------------- /wrappers/igv-reports/test/alignments.bam: -------------------------------------------------------------------------------- 1 | upstream/test/data/minigenome/alignments.bam -------------------------------------------------------------------------------- /wrappers/picard/collecthsmetrics/test/genome.fasta: -------------------------------------------------------------------------------- 1 | >Sheila 2 | GCTAGCTCAGAAAAAAAAAA 3 | -------------------------------------------------------------------------------- /wrappers/samtools/mpileup/test/genome.fasta.fai: -------------------------------------------------------------------------------- 1 | ref 45 5 45 46 2 | ref2 40 57 40 41 3 | -------------------------------------------------------------------------------- /pbs_profile/pbs_jobscript.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | # properties = {properties} 3 | {exec_job} 4 | -------------------------------------------------------------------------------- /wrappers/gatk/baserecalibrator/test/genome.fasta.fai: -------------------------------------------------------------------------------- 1 | ref 45 5 45 46 2 | ref2 40 57 40 41 3 | -------------------------------------------------------------------------------- /wrappers/gatk/genotypegvcfs/test/genome.fasta.fai: -------------------------------------------------------------------------------- 1 | ref 45 5 45 46 2 | ref2 40 57 40 41 3 | -------------------------------------------------------------------------------- /wrappers/gatk/haplotypecaller/test/genome.fasta.fai: -------------------------------------------------------------------------------- 1 | ref 45 5 45 46 2 | ref2 40 57 40 41 3 | -------------------------------------------------------------------------------- /wrappers/gatk/mutect/test/genome/genome.fasta.fai: 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-------------------------------------------------------------------------------- /slurm_profile/slurm-jobscript.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # properties = {properties} 3 | {exec_job} 4 | -------------------------------------------------------------------------------- /wrappers/bwa/aln/test/genome.sa: -------------------------------------------------------------------------------- 1 | ( ( -------------------------------------------------------------------------------- /wrappers/bwa/mem/test/genome.sa: -------------------------------------------------------------------------------- 1 | ( ( -------------------------------------------------------------------------------- /wrappers/bwa/sampe/test/genome.sa: -------------------------------------------------------------------------------- 1 | ( ( -------------------------------------------------------------------------------- /wrappers/bwa/samse/test/genome.sa: -------------------------------------------------------------------------------- 1 | ( ( -------------------------------------------------------------------------------- /envs/rtg.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - conda-forge 3 | - bioconda 4 | dependencies: 5 | - rtg-tools ==3.12 -------------------------------------------------------------------------------- /scripts/SVRecords/__init__.py: -------------------------------------------------------------------------------- 1 | from .SVGrouper import SVGrouper 2 | from .SVAnnotator import SVAnnotator -------------------------------------------------------------------------------- /wrappers/bedtools/slop/test/A.bed: -------------------------------------------------------------------------------- 1 | 1 100 200 2 | 1 150 250 3 | 2 100 200 4 | 2 150 250 5 | 2 200 300 6 | -------------------------------------------------------------------------------- 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channels: 2 | - bioconda 3 | - conda-forge 4 | dependencies: 5 | - samtools ==1.10 6 | -------------------------------------------------------------------------------- /wrappers/samtools/mpileup/test/mapped/a.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ccmbioinfo/crg2/HEAD/wrappers/samtools/mpileup/test/mapped/a.bam -------------------------------------------------------------------------------- /wrappers/bcftools/call/meta.yaml: -------------------------------------------------------------------------------- 1 | name: bcftools call 2 | description: Call variants with bcftools. 3 | authors: 4 | - Johannes Köster 5 | -------------------------------------------------------------------------------- /wrappers/bedtools/bamtofastq/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | dependencies: 4 | - bedtools =2.29.0 5 | - pysam =0.10.0 6 | -------------------------------------------------------------------------------- /wrappers/bwa/aln/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - bwa ==0.7.17 7 | -------------------------------------------------------------------------------- /wrappers/bwa/index/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - bwa ==0.7.17 7 | -------------------------------------------------------------------------------- /wrappers/bwa/sampe/meta.yaml: -------------------------------------------------------------------------------- 1 | name: "bwa sampe" 2 | description: Map paired-end reads with bwa sampe. 3 | authors: 4 | - Julian de Ruiter 5 | -------------------------------------------------------------------------------- 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authors: 4 | - Dennis Kao 5 | -------------------------------------------------------------------------------- /wrappers/vcftools/filter/meta.yaml: -------------------------------------------------------------------------------- 1 | name: vcftools filter 2 | description: Filter vcf files using vcftools 3 | authors: 4 | - Patrik Smeds 5 | -------------------------------------------------------------------------------- /wrappers/vep/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - conda-forge 3 | - bioconda 4 | - defaults 5 | dependencies: 6 | - ensembl-vep =113.3 7 | -------------------------------------------------------------------------------- /wrappers/vt/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda/label/cf201901 3 | - conda-forge 4 | dependencies: 5 | - vt ==2015.11.10 6 | 7 | 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-------------------------------------------------------------------------------- /wrappers/snpeff/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | dependencies: 5 | - snpeff ==4.3.1t 6 | - bcftools =1.9 7 | -------------------------------------------------------------------------------- /wrappers/tabix/meta.yaml: -------------------------------------------------------------------------------- 1 | name: tabix 2 | description: Process given file with tabix (e.g., create index). 3 | authors: 4 | - Johannes Köster 5 | -------------------------------------------------------------------------------- /wrappers/vcfanno/meta.yaml: -------------------------------------------------------------------------------- 1 | name: "snpeff" 2 | description: Annotate a vcf with other VCFs, BEDs, tabixed files 3 | authors: 4 | - Dennis Kao 5 | -------------------------------------------------------------------------------- /envs/coverage.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - conda-forge 3 | - bioconda 4 | dependencies: 5 | - python ==2.7.15 6 | - bedtools ==2.29.0 7 | - numpy >1.1 -------------------------------------------------------------------------------- /wrappers/bcftools/annotate/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - bcftools ==1.9 7 | -------------------------------------------------------------------------------- /wrappers/bcftools/concat/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - bcftools ==1.9 7 | -------------------------------------------------------------------------------- /wrappers/bcftools/filter/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - bcftools ==1.9 7 | -------------------------------------------------------------------------------- /wrappers/bcftools/index/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - bcftools ==1.9 7 | -------------------------------------------------------------------------------- /wrappers/bcftools/merge/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - bcftools ==1.9 7 | -------------------------------------------------------------------------------- /wrappers/bcftools/reheader/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - bcftools ==1.9 7 | -------------------------------------------------------------------------------- /wrappers/bcftools/stats/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - bcftools ==1.9 7 | -------------------------------------------------------------------------------- /wrappers/bcftools/view/meta.yaml: -------------------------------------------------------------------------------- 1 | name: bcftools view 2 | description: View vcf/bcf file in a different format. 3 | authors: 4 | - Johannes Köster 5 | -------------------------------------------------------------------------------- /wrappers/bedtools/merge/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - bedtools =2.29.0 7 | -------------------------------------------------------------------------------- /wrappers/bedtools/slop/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - bedtools =2.29.0 7 | -------------------------------------------------------------------------------- /wrappers/gatk/combinegvcfs/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - gatk4 ==4.1.4.1 7 | -------------------------------------------------------------------------------- /wrappers/gatk3/haplotypecaller/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - gatk ==3.8 7 | -------------------------------------------------------------------------------- /wrappers/manta/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | dependencies: 4 | - manta ==1.6.0 5 | - bcftools ==1.9 6 | - openssl ==1.1.1d 7 | -------------------------------------------------------------------------------- /wrappers/picard/collecthsmetrics/test/mapped/a.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ccmbioinfo/crg2/HEAD/wrappers/picard/collecthsmetrics/test/mapped/a.bam -------------------------------------------------------------------------------- /wrappers/picard/gathervcfs/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - picard ==2.9.2 7 | -------------------------------------------------------------------------------- /wrappers/picard/mergevcfs/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - picard ==2.9.2 7 | -------------------------------------------------------------------------------- /wrappers/picard/revertsam/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - picard ==2.18.16 7 | -------------------------------------------------------------------------------- /wrappers/picard/sortsam/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - picard ==2.9.2 7 | -------------------------------------------------------------------------------- /wrappers/samtools/bam2fq/separate/test/mapped/a.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ccmbioinfo/crg2/HEAD/wrappers/samtools/bam2fq/separate/test/mapped/a.bam -------------------------------------------------------------------------------- /wrappers/samtools/faidx/test/genome.fa: -------------------------------------------------------------------------------- 1 | >ref 2 | AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT 3 | >ref2 4 | aggttttataaaacaattaagtctacagagcaactacgcg 5 | -------------------------------------------------------------------------------- /wrappers/samtools/idxstats/test/mapped/a.sorted.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ccmbioinfo/crg2/HEAD/wrappers/samtools/idxstats/test/mapped/a.sorted.bam -------------------------------------------------------------------------------- /wrappers/vcftools/filter/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - vcftools ==0.1.16 7 | -------------------------------------------------------------------------------- /wrappers/verifybamid2/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - verifybamid2==2.0.1 7 | -------------------------------------------------------------------------------- /wrappers/vt/meta.yaml: -------------------------------------------------------------------------------- 1 | name: "vt" 2 | description: A tool set for short variant discovery in genetic sequence data 3 | authors: 4 | - Dennis Kao 5 | -------------------------------------------------------------------------------- /wrappers/bcftools/concat/meta.yaml: -------------------------------------------------------------------------------- 1 | name: bcftools concat 2 | description: Concatenate vcf/bcf files with bcftools. 3 | authors: 4 | - Johannes Köster 5 | -------------------------------------------------------------------------------- /wrappers/bedtools/coveragebed/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - bedtools ==2.29.0 7 | -------------------------------------------------------------------------------- /wrappers/gatk/baserecalibrator/test/dbsnp.vcf.gz.tbi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ccmbioinfo/crg2/HEAD/wrappers/gatk/baserecalibrator/test/dbsnp.vcf.gz.tbi -------------------------------------------------------------------------------- /wrappers/gatk/combinegvcfs/test/genome.fasta: -------------------------------------------------------------------------------- 1 | >ref 2 | AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT 3 | >ref2 4 | aggttttataaaacaattaagtctacagagcaactacgcg 5 | -------------------------------------------------------------------------------- /wrappers/gatk/filtermutectcalls/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - gatk4 ==4.1.4.1 7 | -------------------------------------------------------------------------------- /wrappers/gatk/genotypegvcfs/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - gatk4 ==4.1.4.1 7 | -------------------------------------------------------------------------------- /wrappers/gatk/haplotypecaller/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - gatk4 ==4.1.4.1 7 | -------------------------------------------------------------------------------- /wrappers/gatk/selectvariants/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - gatk4 ==4.1.4.1 7 | -------------------------------------------------------------------------------- /wrappers/gatk/splitncigarreads/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - gatk4 ==4.1.4.1 7 | -------------------------------------------------------------------------------- /wrappers/gatk/variantfiltration/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - gatk4 ==4.1.4.1 7 | -------------------------------------------------------------------------------- /wrappers/gatk3/realignertargetcreator/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - gatk ==3.8 -------------------------------------------------------------------------------- /wrappers/peddy/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - tabix =0.2.6 7 | - peddy =0.4.1 -------------------------------------------------------------------------------- /wrappers/picard/markduplicates/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - picard ==2.9.2 7 | -------------------------------------------------------------------------------- /wrappers/picard/mergesamfiles/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - picard ==2.9.2 7 | -------------------------------------------------------------------------------- /wrappers/picard/samtofastq/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - picard ==2.18.16 7 | -------------------------------------------------------------------------------- /wrappers/rtg-tools/vcfeval/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - rtg-tools ==3.12 7 | -------------------------------------------------------------------------------- /wrappers/samtools/mpileup/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | dependencies: 5 | - samtools ==1.10 6 | - pigz ==2.3.4 7 | -------------------------------------------------------------------------------- /wrappers/samtools/mpileup/test/genome.fasta: -------------------------------------------------------------------------------- 1 | >ref 2 | AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT 3 | >ref2 4 | aggttttataaaacaattaagtctacagagcaactacgcg 5 | -------------------------------------------------------------------------------- /wrappers/snpeff/meta.yaml: -------------------------------------------------------------------------------- 1 | name: "snpeff" 2 | description: Annotate predicted effect of nucleotide changes with SnpEff 3 | authors: 4 | - Bradford Powell 5 | -------------------------------------------------------------------------------- /wrappers/vcf2db/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | dependencies: 4 | - vcf2db =2018.10.26 5 | - bcftools =1.11 6 | - decorator =4.4.2 7 | -------------------------------------------------------------------------------- /wrappers/bcftools/reheader/meta.yaml: -------------------------------------------------------------------------------- 1 | name: bcftools reheader 2 | description: Change header or sample names of vcf/bcf file. 3 | authors: 4 | - Jan Forster 5 | -------------------------------------------------------------------------------- /wrappers/bedtools/intersect/meta.yaml: -------------------------------------------------------------------------------- 1 | name: "bedtools intersect" 2 | description: Intersect BED/BAM/VCF files with bedtools. 3 | authors: 4 | - Jan Forster 5 | -------------------------------------------------------------------------------- /wrappers/gatk/baserecalibrator/test/genome.fasta: -------------------------------------------------------------------------------- 1 | >ref 2 | AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT 3 | >ref2 4 | aggttttataaaacaattaagtctacagagcaactacgcg 5 | -------------------------------------------------------------------------------- /wrappers/gatk/genotypegvcfs/test/genome.fasta: -------------------------------------------------------------------------------- 1 | >ref 2 | AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT 3 | >ref2 4 | aggttttataaaacaattaagtctacagagcaactacgcg 5 | -------------------------------------------------------------------------------- /wrappers/gatk/haplotypecaller/test/genome.fasta: -------------------------------------------------------------------------------- 1 | >ref 2 | AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT 3 | >ref2 4 | aggttttataaaacaattaagtctacagagcaactacgcg 5 | -------------------------------------------------------------------------------- /wrappers/gatk/mutect/test/genome/genome.fasta: -------------------------------------------------------------------------------- 1 | >ref 2 | AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT 3 | >ref2 4 | aggttttataaaacaattaagtctacagagcaactacgcg 5 | -------------------------------------------------------------------------------- /wrappers/gatk/selectvariants/test/genome.fasta: -------------------------------------------------------------------------------- 1 | >ref 2 | AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT 3 | >ref2 4 | aggttttataaaacaattaagtctacagagcaactacgcg 5 | -------------------------------------------------------------------------------- /wrappers/gatk/splitncigarreads/test/genome.fasta: -------------------------------------------------------------------------------- 1 | >ref 2 | AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT 3 | >ref2 4 | aggttttataaaacaattaagtctacagagcaactacgcg 5 | -------------------------------------------------------------------------------- /wrappers/gatk/variantfiltration/test/genome.fasta: -------------------------------------------------------------------------------- 1 | >ref 2 | AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT 3 | >ref2 4 | aggttttataaaacaattaagtctacagagcaactacgcg 5 | -------------------------------------------------------------------------------- /wrappers/gatk/variantrecalibrator/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - gatk4 ==4.1.4.1 7 | -------------------------------------------------------------------------------- /wrappers/gatk3/haplotypecaller/test/genome.fasta: -------------------------------------------------------------------------------- 1 | >ref 2 | AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT 3 | >ref2 4 | aggttttataaaacaattaagtctacagagcaactacgcg 5 | -------------------------------------------------------------------------------- /wrappers/samtools/bam2fq/interleaved/test/mapped/a.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ccmbioinfo/crg2/HEAD/wrappers/samtools/bam2fq/interleaved/test/mapped/a.bam -------------------------------------------------------------------------------- /wrappers/samtools/idxstats/test/mapped/a.sorted.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ccmbioinfo/crg2/HEAD/wrappers/samtools/idxstats/test/mapped/a.sorted.bam.bai -------------------------------------------------------------------------------- /units.tsv: -------------------------------------------------------------------------------- 1 | sample platform fq1 fq2 bam cram 2 | NA12878 ILLUMINA /hpf/largeprojects/ccmbio/GIAB_benchmark_datasets/hg19/WGS/NA12878/RMNISTHS_30xdownsample.bam 3 | -------------------------------------------------------------------------------- /wrappers/freebayes/meta.yaml: -------------------------------------------------------------------------------- 1 | name: "freebayes" 2 | description: Call small genomic variants with freebayes. 3 | authors: 4 | - Johannes Köster 5 | - Felix Mölder -------------------------------------------------------------------------------- /wrappers/picard/addorreplacereadgroups/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - picard ==2.9.2 7 | -------------------------------------------------------------------------------- /wrappers/picard/collectinsertsizemetrics/test/mapped/a.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ccmbioinfo/crg2/HEAD/wrappers/picard/collectinsertsizemetrics/test/mapped/a.bam -------------------------------------------------------------------------------- /wrappers/picard/collecttargetedpcrmetrics/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - picard ==2.9.2 7 | -------------------------------------------------------------------------------- /wrappers/picard/createsequencedictionary/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - picard ==2.9.2 7 | -------------------------------------------------------------------------------- /envs/hpo_to_panel.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - conda-forge 3 | - bioconda 4 | dependencies: 5 | - python=3.9.4 6 | - pandas=1.2.4 7 | - pyranges 8 | - pybedtools 9 | -------------------------------------------------------------------------------- /rules/multiqc_config.yaml: -------------------------------------------------------------------------------- 1 | table_columns_visible: 2 | Peddy: 3 | error_sex_check: False 4 | family_id: False 5 | FastQC: 6 | percent_duplicates: False 7 | -------------------------------------------------------------------------------- /wrappers/bedtools/intersect/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - bedtools =2.29.0 7 | - tabix 8 | -------------------------------------------------------------------------------- /wrappers/bwa/sampe/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | dependencies: 5 | - bwa ==0.7.17 6 | - samtools ==1.9 7 | - picard ==2.20.1 8 | -------------------------------------------------------------------------------- /wrappers/bwa/samse/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | dependencies: 5 | - bwa ==0.7.17 6 | - samtools ==1.9 7 | - picard ==2.20.1 8 | -------------------------------------------------------------------------------- /wrappers/gatk/baserecalibrator/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - gatk4 ==4.1.4.1 7 | - openjdk =8 -------------------------------------------------------------------------------- /wrappers/picard/collectalignmentsummarymetrics/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - picard ==2.9.2 7 | -------------------------------------------------------------------------------- /wrappers/picard/collecttargetedpcrmetrics/test/mapped/a.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ccmbioinfo/crg2/HEAD/wrappers/picard/collecttargetedpcrmetrics/test/mapped/a.bam -------------------------------------------------------------------------------- /wrappers/picard/createsequencedictionary/test/genome.fasta: -------------------------------------------------------------------------------- 1 | >ref 2 | AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT 3 | >ref2 4 | aggttttataaaacaattaagtctacagagcaactacgcg 5 | -------------------------------------------------------------------------------- /wrappers/samblaster/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - samtools ==1.9 7 | - samblaster ==0.1.25 8 | -------------------------------------------------------------------------------- /wrappers/samtools/fixmate/environment.yaml: -------------------------------------------------------------------------------- 1 | name: samtools 2 | channels: 3 | - bioconda 4 | - conda-forge 5 | - defaults 6 | dependencies: 7 | - samtools ==1.10 8 | -------------------------------------------------------------------------------- /envs/eh-report.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - conda-forge 3 | - bioconda 4 | dependencies: 5 | - python=3.7.8 6 | - python-docx=0.8.10 7 | - pandas=1.1.2 8 | - xlsxwriter=1.3.7 -------------------------------------------------------------------------------- /wrappers/reference/ensembl-variation/test/refs/variation.vcf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ccmbioinfo/crg2/HEAD/wrappers/reference/ensembl-variation/test/refs/variation.vcf.gz -------------------------------------------------------------------------------- /wrappers/rtg-tools/vcfsubset/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - rtg-tools ==3.12 7 | - bcftools ==1.11 -------------------------------------------------------------------------------- /wrappers/samtools/depth/meta.yaml: -------------------------------------------------------------------------------- 1 | name: samtools depth 2 | description: Compute the read depth at each position or region using samtools. 3 | authors: 4 | - Dayne Filer 5 | -------------------------------------------------------------------------------- /envs/common.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - conda-forge 3 | - bioconda 4 | dependencies: 5 | - tabix ==0.2.6 6 | - bcftools ==1.9 7 | - parallel==20190522 8 | - bedtools==2.29.0 9 | -------------------------------------------------------------------------------- /wrappers/bedtools/merge/meta.yaml: -------------------------------------------------------------------------------- 1 | name: "bedtools merge" 2 | description: Merge entries in one or multiple BED/BAM/VCF/GFF files with bedtools. 3 | authors: 4 | - Jan Forster 5 | -------------------------------------------------------------------------------- /wrappers/bedtools/slop/meta.yaml: -------------------------------------------------------------------------------- 1 | name: "bedtools slop" 2 | description: Increase the size of each feature in a BED/BAM/VCF by a specified factor. 3 | authors: 4 | - Jan Forster 5 | -------------------------------------------------------------------------------- /wrappers/picard/collectalignmentsummarymetrics/test/mapped/a.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ccmbioinfo/crg2/HEAD/wrappers/picard/collectalignmentsummarymetrics/test/mapped/a.bam -------------------------------------------------------------------------------- /slurm_profile/settings.json: -------------------------------------------------------------------------------- 1 | { 2 | "SBATCH_DEFAULTS": "", 3 | "CLUSTER_NAME": "", 4 | "CLUSTER_CONFIG": "slurm-config.yaml", 5 | "ADVANCED_ARGUMENT_CONVERSION": "no" 6 | } -------------------------------------------------------------------------------- /wrappers/bwa/mem/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - bwa ==0.7.17 7 | - samtools ==1.9 8 | - picard ==2.20.1 9 | -------------------------------------------------------------------------------- /wrappers/multiqc/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - multiqc ==1.7 7 | - python ==3.7 8 | - pyyaml ==5.4.1 9 | -------------------------------------------------------------------------------- /wrappers/picard/collecthsmetrics/test/regions.intervals: -------------------------------------------------------------------------------- 1 | @HD VN:1.5 SO:coordinate 2 | @SQ SN:Sheila LN:20 M5:7ddd8a4b4f2c1dec43476a738b1a9b72 UR:file:genome.fasta 3 | Sheila 6 15 + . 4 | -------------------------------------------------------------------------------- /wrappers/picard/collecttargetedpcrmetrics/test/target.list: -------------------------------------------------------------------------------- 1 | @HD VN:1.5 SO:coordinate 2 | @SQ SN:Sheila LN:20 M5:7ddd8a4b4f2c1dec43476a738b1a9b72 UR:file:genome.fasta 3 | Sheila 6 15 + . 4 | -------------------------------------------------------------------------------- /wrappers/reference/ensembl-variation/test/refs/variation.vcf.gz.tbi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ccmbioinfo/crg2/HEAD/wrappers/reference/ensembl-variation/test/refs/variation.vcf.gz.tbi -------------------------------------------------------------------------------- /wrappers/smoove/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - smoove ==0.2.5 7 | - svtyper ==0.7.0 8 | - bcftools ==1.5 9 | -------------------------------------------------------------------------------- /wrappers/picard/collectinsertsizemetrics/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - picard ==2.9.2 7 | - r-base ==3.3.2 8 | -------------------------------------------------------------------------------- /wrappers/picard/collecttargetedpcrmetrics/test/amplicon.list: -------------------------------------------------------------------------------- 1 | @HD VN:1.5 SO:coordinate 2 | @SQ SN:Sheila LN:20 M5:7ddd8a4b4f2c1dec43476a738b1a9b72 UR:file:genome.fasta 3 | Sheila 8 13 + . 4 | -------------------------------------------------------------------------------- /wrappers/bcftools/call/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - samtools ==1.9 7 | - bcftools ==1.9 8 | - parallel ==20190522 -------------------------------------------------------------------------------- /wrappers/samtools/bam2fq/separate/test/reads/a.1.fq: -------------------------------------------------------------------------------- 1 | @a1 2 | AAAAAAAAAA 3 | + 4 | ********** 5 | @b1 6 | AAAAAAAAAA 7 | + 8 | ********** 9 | @c1 10 | AAAAAAAAAA 11 | + 12 | ********** 13 | -------------------------------------------------------------------------------- /wrappers/samtools/bam2fq/separate/test/reads/a.2.fq: -------------------------------------------------------------------------------- 1 | @a1 2 | AAAAAAATAA 3 | + 4 | ********** 5 | @b1 6 | AAAAAAATAA 7 | + 8 | ********** 9 | @c1 10 | AAAAAAATAA 11 | + 12 | ********** 13 | -------------------------------------------------------------------------------- /envs/melt.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | dependencies: 5 | - python >3.5 6 | - java-jdk >=1.8 7 | - bowtie2 8 | - snpeff ==4.3.1t 9 | - bcftools ==1.9 10 | -------------------------------------------------------------------------------- /wrappers/report_upload/post_report/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - python >3.5 7 | - pandas ==1.1.0 8 | - numpy >1.1 9 | -------------------------------------------------------------------------------- /wrappers/samtools/fastq/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | dependencies: 5 | - pysam ==0.15.3 6 | - numpy ==1.20.0 7 | - pandas ==1.1.0 8 | - samtools ==1.10 9 | -------------------------------------------------------------------------------- /wrappers/bwa/mem-samblaster/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - bwa ==0.7.17 7 | - sambamba ==0.7.1 8 | - samblaster ==0.1.24 9 | -------------------------------------------------------------------------------- /wrappers/bwa/mem/meta.yaml: -------------------------------------------------------------------------------- 1 | name: "bwa mem" 2 | description: Map reads using bwa mem, with optional sorting using 3 | samtools or picard. 4 | authors: 5 | - Johannes Köster 6 | - Julian de Ruiter 7 | -------------------------------------------------------------------------------- /wrappers/igv-reports/meta.yaml: -------------------------------------------------------------------------------- 1 | name: igv-reports 2 | description: Create self-contained igv.js HTML pages. 3 | authors: 4 | - Johannes Köster 5 | input: 6 | - BAM, VCF, ... 7 | output: 8 | - HTML 9 | -------------------------------------------------------------------------------- /wrappers/platypus/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - platypus-variant ==0.8.1.2 7 | - vcflib ==1.0.0_rc2 8 | - picard ==2.9.2 9 | -------------------------------------------------------------------------------- /wrappers/bedtools/coveragebed/meta.yaml: -------------------------------------------------------------------------------- 1 | name: "coverageBed" 2 | description: 3 | Returns the depth and breadth of coverage of features from B 4 | on the intervals in A. 5 | authors: 6 | - Patrik Smeds 7 | -------------------------------------------------------------------------------- /wrappers/bwa/mem-samblaster/meta.yaml: -------------------------------------------------------------------------------- 1 | name: "bwa mem samblaster" 2 | description: Map reads using bwa mem, mark duplicates by samblaster and sort and index by sambamba. 3 | authors: 4 | - Christopher Schröder -------------------------------------------------------------------------------- /wrappers/samtools/index/meta.yaml: -------------------------------------------------------------------------------- 1 | name: samtools index 2 | description: Index bam file with samtools. 3 | authors: 4 | - Johannes Köster 5 | input: 6 | - bam file 7 | output: 8 | - bam file index (.bai) 9 | -------------------------------------------------------------------------------- /wrappers/picard/collectalignmentsummarymetrics/meta.yaml: -------------------------------------------------------------------------------- 1 | name: picard CollectAlignmentSummaryMetrics 2 | description: | 3 | Collect metrics on aligned reads with picard tools. 4 | authors: 5 | - Johannes Köster 6 | -------------------------------------------------------------------------------- /wrappers/samtools/view/wrapper.py: -------------------------------------------------------------------------------- 1 | from snakemake.shell import shell 2 | 3 | 4 | shell( 5 | "samtools view -T {snakemake.input.ref} -@ {snakemake.threads} -C -o {snakemake.output} {snakemake.input.bam}" 6 | ) 7 | -------------------------------------------------------------------------------- /envs/ehdn_outlier.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | dependencies: 5 | - python=3.7.8 6 | - python-docx=0.8.10 7 | - pandas=1.1.2 8 | - numpy 9 | - matplotlib 10 | - xlsxwriter=1.3.7 -------------------------------------------------------------------------------- /wrappers/report_upload/PT_identifier/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - python >3.7 7 | - pandas ==1.1.0 8 | - numpy >1.1 9 | - requests ==2.28.1 -------------------------------------------------------------------------------- /wrappers/picard/collecttargetedpcrmetrics/meta.yaml: -------------------------------------------------------------------------------- 1 | name: picard CollectTargetedPcrMetrics 2 | description: | 3 | Collect metric information for target pcr metrics runs, with picard tools. 4 | authors: 5 | - Patrik Smeds 6 | -------------------------------------------------------------------------------- /wrappers/reference/ensembl-sequence/meta.yaml: -------------------------------------------------------------------------------- 1 | name: ensembl-sequence 2 | description: Download sequences (e.g. genome) from ENSEMBL FTP servers, and store them in a single .fasta file. 3 | authors: 4 | - Johannes Köster 5 | -------------------------------------------------------------------------------- /wrappers/reference/ensembl-variation/meta.yaml: -------------------------------------------------------------------------------- 1 | name: ensembl-variation 2 | description: Download known genomic variants from ENSEMBL FTP servers, and store them in a single .vcf.gz file. 3 | authors: 4 | - Johannes Köster 5 | -------------------------------------------------------------------------------- /wrappers/fastq_screen/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - fastq-screen ==0.13.0 7 | - bowtie2 ==2.4.1 8 | - libwebp ==0.5.2 9 | - libiconv ==1.16 10 | -------------------------------------------------------------------------------- /wrappers/picard/mergevcfs/meta.yaml: -------------------------------------------------------------------------------- 1 | name: picard MergeVcfs 2 | description: | 3 | Merge vcf files using picard tools. 4 | authors: 5 | - Johannes Köster 6 | input: 7 | - vcf files 8 | output: 9 | - merged vcf file 10 | -------------------------------------------------------------------------------- /wrappers/picard/samtofastq/meta.yaml: -------------------------------------------------------------------------------- 1 | name: picard SomToFastq 2 | description: | 3 | Converts a SAM or BAM file to FASTQ. 4 | authors: 5 | - Patrik Smeds 6 | input: 7 | - sam/bam file 8 | output: 9 | - fastq files. 10 | -------------------------------------------------------------------------------- /wrappers/samtools/flagstat/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule samtools_flagstat: 2 | input: 3 | "mapped/{sample}.bam" 4 | output: 5 | "mapped/{sample}.bam.flagstat" 6 | wrapper: 7 | "master/bio/samtools/flagstat" 8 | -------------------------------------------------------------------------------- /wrappers/gatk3/printreads/test/README.md: -------------------------------------------------------------------------------- 1 | Note that the conda gatk3 recipe requires manual intervention, as the gatk3 jar 2 | have to be provided by the user due to license restrictions. Therefore this test 3 | can't be run with circleci. 4 | -------------------------------------------------------------------------------- /wrappers/multiqc/meta.yaml: -------------------------------------------------------------------------------- 1 | name: multiqc 2 | description: | 3 | Generate qc report using multiqc. 4 | authors: 5 | - Julian de Ruiter 6 | input: 7 | - input directory containing qc files 8 | output: 9 | - qc report (html) 10 | -------------------------------------------------------------------------------- /wrappers/picard/sortsam/meta.yaml: -------------------------------------------------------------------------------- 1 | name: picard SortSam 2 | description: | 3 | Sort sam/bam files using picard tools. 4 | authors: 5 | - Julian de Ruiter 6 | input: 7 | - sam/bam file 8 | output: 9 | - sorted sam/bam file. 10 | -------------------------------------------------------------------------------- /wrappers/gatk3/baserecalibrator/test/README.md: -------------------------------------------------------------------------------- 1 | Note that the conda gatk3 recipe requires manual intervention, as the gatk3 jar 2 | have to be provided by the user due to license restrictions. Therefore this test 3 | can't be run with circleci. 4 | -------------------------------------------------------------------------------- /wrappers/gatk3/indelrealigner/test/README.md: -------------------------------------------------------------------------------- 1 | Note that the conda gatk3 recipe requires manual intervention, as the gatk3 jar 2 | have to be provided by the user due to license restrictions. Therefore this test 3 | can't be run with circleci. 4 | -------------------------------------------------------------------------------- /wrappers/picard/revertsam/meta.yaml: -------------------------------------------------------------------------------- 1 | name: picard RevertSam 2 | description: | 3 | Reverts SAM or BAM files to a previous state. . 4 | authors: 5 | - Patrik Smeds 6 | input: 7 | - sam/bam file 8 | output: 9 | - sam/bam file. 10 | -------------------------------------------------------------------------------- /wrappers/gatk3/realignertargetcreator/test/README.md: -------------------------------------------------------------------------------- 1 | Note that the conda gatk3 recipe requires manual intervention, as the gatk3 jar 2 | have to be provided by the user due to license restrictions. Therefore this test 3 | can't be run with circleci. 4 | -------------------------------------------------------------------------------- /wrappers/freebayes/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | dependencies: 5 | - freebayes ==1.3.1 6 | - bcftools ==1.10 7 | - parallel ==20190522 8 | - bedtools >=2.29 9 | - sed ==4.7 10 | - vcflib ==1.0.0_rc2 -------------------------------------------------------------------------------- /wrappers/picard/mergesamfiles/meta.yaml: -------------------------------------------------------------------------------- 1 | name: picard MergeSamFiles 2 | description: | 3 | Merge sam/bam files using picard tools. 4 | authors: 5 | - Julian de Ruiter 6 | input: 7 | - sam/bam files 8 | output: 9 | - merged sam/bam file 10 | -------------------------------------------------------------------------------- /envs/mt_report.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | dependencies: 5 | - python > 3.5.4 6 | - pandas==1.0.1 7 | - pysam==0.15.3 8 | - python-dateutil==2.8.0 9 | - pyvcf==0.6.8 10 | - xlsxwriter==1.1.8 11 | - openpyxl==3.0.3 -------------------------------------------------------------------------------- /wrappers/reference/ensembl-annotation/meta.yaml: -------------------------------------------------------------------------------- 1 | name: ensembl-annotation 2 | description: Download annotation of genomic sites (e.g. transcripts) from ENSEMBL FTP servers, and store them in a single .gtf or .gff3 file. 3 | authors: 4 | - Johannes Köster 5 | -------------------------------------------------------------------------------- /wrappers/verifybamid2/meta.yaml: -------------------------------------------------------------------------------- 1 | name: verifybamid2 2 | description: detects sample contamination using previously known genotypes 3 | authors: Delvin So 4 | input: sorted bam file 5 | output: sample statistics on how much the sample matches known provided samples -------------------------------------------------------------------------------- /wrappers/bcftools/norm/meta.yaml: -------------------------------------------------------------------------------- 1 | name: bcftools norm 2 | description: Left-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; recover multiallelics from multiple rows. 3 | authors: 4 | - Dayne Filer 5 | -------------------------------------------------------------------------------- /wrappers/picard/createsequencedictionary/meta.yaml: -------------------------------------------------------------------------------- 1 | name: picard CreateSequenceDictionary 2 | description: | 3 | Create a .dict file for a given FASTA file 4 | authors: 5 | - Johannes Köster 6 | input: 7 | - FASTA file 8 | output: 9 | - .dict file 10 | -------------------------------------------------------------------------------- /wrappers/samtools/faidx/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule samtools_index: 2 | input: 3 | "{sample}.fa" 4 | output: 5 | "{sample}.fa.fai" 6 | params: 7 | "" # optional params string 8 | wrapper: 9 | "master/bio/samtools/faidx" 10 | -------------------------------------------------------------------------------- /wrappers/samtools/fixmate/meta.yaml: -------------------------------------------------------------------------------- 1 | name: samtools fixmate 2 | description: Use samtools to correct mate information after BWA mapping. 3 | authors: 4 | - Thibault Dayris 5 | input: 6 | - bam or sam file (.bam,.sam) 7 | output: 8 | - bam or sam file (.bam,.sam) 9 | -------------------------------------------------------------------------------- /wrappers/samtools/sort/meta.yaml: -------------------------------------------------------------------------------- 1 | name: samtools sort 2 | description: Sort bam file with samtools. 3 | authors: 4 | - Johannes Köster 5 | notes: | 6 | * Samtools -@/--threads takes one integer as input. This is the number of additional threads and not raw threads. 7 | -------------------------------------------------------------------------------- /wrappers/samtools/view/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule samtools_view: 2 | input: 3 | "{sample}.sam" 4 | output: 5 | "{sample}.bam" 6 | params: 7 | "-b" # optional params string 8 | wrapper: 9 | "master/bio/samtools/view" 10 | -------------------------------------------------------------------------------- /wrappers/picard/gathervcfs/meta.yaml: -------------------------------------------------------------------------------- 1 | name: picard MergeVcfs 2 | description: | 3 | Gathers multiple VCF files from a scatter operation into a single VCF file. 4 | authors: 5 | - Johannes Köster 6 | input: 7 | - vcf files 8 | output: 9 | - merged vcf file 10 | -------------------------------------------------------------------------------- /wrappers/samtools/flagstat/meta.yaml: -------------------------------------------------------------------------------- 1 | name: samtools flagstat 2 | description: Use samtools to create a flagstat file from a bam or sam file. 3 | authors: 4 | - Christopher Preusch 5 | input: 6 | - bam or sam file (.bam,.sam) 7 | output: 8 | - flagstat file (.flagstat) 9 | -------------------------------------------------------------------------------- /wrappers/fastqc/meta.yaml: -------------------------------------------------------------------------------- 1 | name: fastqc 2 | description: | 3 | Generate fastq qc statistics using fastqc. 4 | authors: 5 | - Julian de Ruiter 6 | input: 7 | - fastq file 8 | output: 9 | - html file containing statistics 10 | - zip file containing statistics 11 | -------------------------------------------------------------------------------- /wrappers/picard/addorreplacereadgroups/meta.yaml: -------------------------------------------------------------------------------- 1 | name: picard AddOrReplaceReadGroups 2 | description: Add or replace read groups with picard tools. 3 | authors: 4 | - Johannes Köster 5 | input: 6 | - bam file 7 | output: 8 | - bam file with added or replaced read groups 9 | -------------------------------------------------------------------------------- /wrappers/qualimap/meta.yaml: -------------------------------------------------------------------------------- 1 | name: qualimap 2 | description: high level overview of sequencing quality to assist in detection of sequencing bias and mapping 3 | authors: Delvin So 4 | input: sorted bam file 5 | output: statistics such as genome coverage, gc content distribution 6 | -------------------------------------------------------------------------------- /envs/ehdn-dbscan.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | dependencies: 5 | - r 6 | - r-dbscan=1.1-8 7 | - r-ggplot2 8 | - r-data.table 9 | - r-doSNOW=1.0.19 10 | - r-cowplot 11 | - bioconductor-genomicranges 12 | - bioconductor-biostrings 13 | -------------------------------------------------------------------------------- /schemas/samples.schema.yaml: -------------------------------------------------------------------------------- 1 | $schema: "http://json-schema.org/draft-04/schema#" 2 | 3 | description: an entry in the sample sheet 4 | properties: 5 | sample: 6 | type: ["number", "string"] 7 | description: sample name/identifier 8 | 9 | required: 10 | - sample 11 | -------------------------------------------------------------------------------- /wrappers/bcftools/index/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule bcftools_index: 2 | input: 3 | "a.bcf" 4 | output: 5 | "a.bcf.csi" 6 | params: 7 | extra="" # optional parameters for bcftools index 8 | wrapper: 9 | "master/bio/bcftools/index" 10 | -------------------------------------------------------------------------------- /wrappers/gatk/mutect/meta.yaml: -------------------------------------------------------------------------------- 1 | name: GATK Mutect2 2 | description: Call somatic SNVs and indels via local assembly of haplotypes 3 | authors: 4 | - Thibault Dayris 5 | input: 6 | - Mapped reads (SAM/BAM/CRAM) 7 | - Reference Fasta file 8 | output: 9 | - Variant file 10 | -------------------------------------------------------------------------------- /wrappers/picard/collecthsmetrics/meta.yaml: -------------------------------------------------------------------------------- 1 | name: picard CollectHSMetrics 2 | description: | 3 | Collects hybrid-selection (HS) metrics for a SAM or BAM file using picard. 4 | authors: 5 | - Julian de Ruiter 6 | input: 7 | - bam file 8 | output: 9 | - metrics file 10 | -------------------------------------------------------------------------------- /wrappers/picard/markduplicates/meta.yaml: -------------------------------------------------------------------------------- 1 | name: picard MarkDuplicates 2 | description: | 3 | Mark PCR and optical duplicates with picard tools. 4 | authors: 5 | - Johannes Köster 6 | input: 7 | - bam file 8 | output: 9 | - bam file with marked or removed duplicates 10 | -------------------------------------------------------------------------------- /wrappers/samtools/faidx/meta.yaml: -------------------------------------------------------------------------------- 1 | name: samtools faidx 2 | description: index reference sequence in FASTA format from reference sequence 3 | authors: 4 | - Michael Chambers 5 | input: 6 | - reference sequence file (.fa) 7 | output: 8 | - indexed reference sequence file (.fai) 9 | -------------------------------------------------------------------------------- /wrappers/vcftools/filter/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule filter_vcf: 2 | input: 3 | "{sample}.vcf" 4 | output: 5 | "{sample}.filtered.vcf" 6 | params: 7 | extra="--chr 1 --recode-INFO-all" 8 | wrapper: 9 | "master/bio/vcftools/filter" 10 | -------------------------------------------------------------------------------- /wrappers/bcftools/norm/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule norm_vcf: 2 | input: 3 | "{prefix}.vcf" 4 | output: 5 | "{prefix}.vcf" 6 | params: 7 | "" # optional parameters for bcftools norm (except -o) 8 | wrapper: 9 | "master/bio/bcftools/norm" 10 | -------------------------------------------------------------------------------- /wrappers/bcftools/view/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule bcf_to_vcf: 2 | input: 3 | "{prefix}.bcf" 4 | output: 5 | "{prefix}.vcf" 6 | params: 7 | "" # optional parameters for bcftools view (except -o) 8 | wrapper: 9 | "master/bio/bcftools/view" 10 | -------------------------------------------------------------------------------- /wrappers/samtools/index/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule samtools_index: 2 | input: 3 | "mapped/{sample}.sorted.bam" 4 | output: 5 | "mapped/{sample}.sorted.bam.bai" 6 | params: 7 | "" # optional params string 8 | wrapper: 9 | "master/bio/samtools/index" 10 | -------------------------------------------------------------------------------- /envs/crg.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - conda-forge 3 | - bioconda 4 | dependencies: 5 | - sqlite >3.2 6 | - python ==3.9 7 | - scikit-allel >1.2 8 | - pybedtools >0.8.0 9 | - numpy ==1.21.2 10 | - pandas ==1.3.3 11 | - bedtools ==2.29.0 12 | - bcftools ==1.12 13 | - pysam ==0.17.0 14 | -------------------------------------------------------------------------------- /wrappers/bcftools/merge/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule bcftools_merge: 2 | input: 3 | calls=["a.bcf", "b.bcf"] 4 | output: 5 | "all.bcf" 6 | params: 7 | "" # optional parameters for bcftools concat (except -o) 8 | wrapper: 9 | "master/bio/bcftools/merge" 10 | -------------------------------------------------------------------------------- /wrappers/bcftools/concat/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule bcftools_concat: 2 | input: 3 | calls=["a.bcf", "b.bcf"] 4 | output: 5 | "all.bcf" 6 | params: 7 | "" # optional parameters for bcftools concat (except -o) 8 | wrapper: 9 | "master/bio/bcftools/concat" 10 | -------------------------------------------------------------------------------- /wrappers/samtools/bam2fq/interleaved/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule samtools_bam2fq_interleaved: 2 | input: 3 | "mapped/{sample}.bam" 4 | output: 5 | "reads/{sample}.fq" 6 | params: 7 | " " 8 | threads: 3 9 | wrapper: 10 | "master/bio/samtools/bam2fq/interleaved" 11 | -------------------------------------------------------------------------------- /wrappers/samtools/bam2fq/interleaved/meta.yaml: -------------------------------------------------------------------------------- 1 | name: samtools bam2fq interleaved 2 | description: 3 | Convert a bam file back to unaligned reads in a single fastq file with 4 | samtools. For paired end reads, this results in an unsorted interleaved file. 5 | authors: 6 | - David Laehnemann 7 | - Victoria Sack 8 | -------------------------------------------------------------------------------- /wrappers/picard/mergevcfs/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule merge_vcfs: 2 | input: 3 | vcfs=["snvs.chr1.vcf", "snvs.chr2.vcf"] 4 | output: 5 | "snvs.vcf" 6 | log: 7 | "logs/picard/mergevcfs.log" 8 | params: 9 | extra="" 10 | wrapper: 11 | "master/bio/picard/mergevcfs" 12 | -------------------------------------------------------------------------------- /envs/svscore.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - conda-forge 3 | - bioconda 4 | 5 | dependencies: 6 | - vt =2015.11.10 7 | - tabix =0.2.6 8 | - vcfanno =0.3.2 9 | - pbgzip =2016.08.04 10 | - svtools =0.5.1 11 | - perl >5.10.1 12 | - perl-list-moreutils =0.428 13 | - perl-math-round =0.07 14 | - perl-findbin =1.51 15 | -------------------------------------------------------------------------------- /wrappers/vcflib/wrapper.py: -------------------------------------------------------------------------------- 1 | 2 | from snakemake.shell import shell 3 | 4 | 5 | log = snakemake.log_fmt_shell(stdout=False, stderr=True) 6 | 7 | shell( 8 | "vcfallelicprimitives -t DECOMPOSED --keep-geno {snakemake.input[0]} " 9 | "| vcffixup - | vcfstreamsort " 10 | " > {snakemake.output[0]} {log}" 11 | ) 12 | -------------------------------------------------------------------------------- /wrappers/samtools/flagstat/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Christopher Preusch" 2 | __copyright__ = "Copyright 2017, Christopher Preusch" 3 | __email__ = "cpreusch[at]ust.hk" 4 | __license__ = "MIT" 5 | 6 | 7 | from snakemake.shell import shell 8 | 9 | 10 | shell("samtools flagstat {snakemake.input[0]} > {snakemake.output[0]}") 11 | -------------------------------------------------------------------------------- /wrappers/vt/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule vt: 2 | input: 3 | "{sample}.vcf", # (vcf, bcf, or vcf.gz) 4 | output: 5 | calls="annnotation/{sample}.uniq.normalized.decomposed.vcf.gz", # annotated calls (vcf, bcf, or vcf.gz) 6 | log: 7 | "logs/vt/{sample}.log" 8 | wrapper: 9 | "master/bio/vt" 10 | -------------------------------------------------------------------------------- /wrappers/tabix/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule tabix: 2 | input: 3 | "{prefix}.vcf.gz" 4 | output: 5 | "{prefix}.vcf.gz.tbi" 6 | params: 7 | # pass arguments to tabix (e.g. index a vcf) 8 | "-p vcf" 9 | log: 10 | "logs/tabix/{prefix}.log" 11 | wrapper: 12 | "master/bio/tabix" 13 | -------------------------------------------------------------------------------- /wrappers/samtools/bam2fq/interleaved/test/reads/a.fq: -------------------------------------------------------------------------------- 1 | @a1/1 2 | AAAAAAAAAA 3 | + 4 | ********** 5 | @b1/1 6 | AAAAAAAAAA 7 | + 8 | ********** 9 | @c1/1 10 | AAAAAAAAAA 11 | + 12 | ********** 13 | @a1/2 14 | AAAAAAAAAA 15 | + 16 | ********** 17 | @b1/2 18 | AAAAAAAAAA 19 | + 20 | ********** 21 | @c1/2 22 | AAAAAAAAAA 23 | + 24 | ********** 25 | -------------------------------------------------------------------------------- /wrappers/samtools/idxstats/meta.yaml: -------------------------------------------------------------------------------- 1 | name: samtools idxstats 2 | description: Use samtools to retrieve and print stats form indexed bam, sam or cram files 3 | authors: 4 | - Antonie Vietor 5 | input: 6 | - indexed sam, bam or cram file (.sam, .bam, .cram) 7 | - corresponding index files 8 | output: 9 | - idxstat file (.idxstats) 10 | -------------------------------------------------------------------------------- /wrappers/samtools/index/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Johannes Köster" 2 | __copyright__ = "Copyright 2016, Johannes Köster" 3 | __email__ = "koester@jimmy.harvard.edu" 4 | __license__ = "MIT" 5 | 6 | 7 | from snakemake.shell import shell 8 | 9 | 10 | shell("samtools index {snakemake.params} {snakemake.input[0]} {snakemake.output[0]}") 11 | -------------------------------------------------------------------------------- /wrappers/bcftools/norm/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Dayne Filer" 2 | __copyright__ = "Copyright 2019, Dayne Filer" 3 | __email__ = "dayne.filer@gmail.com" 4 | __license__ = "MIT" 5 | 6 | 7 | from snakemake.shell import shell 8 | 9 | 10 | shell( 11 | "bcftools norm {snakemake.params} {snakemake.input[0]} " "-o {snakemake.output[0]}" 12 | ) 13 | -------------------------------------------------------------------------------- /wrappers/picard/collectinsertsizemetrics/meta.yaml: -------------------------------------------------------------------------------- 1 | name: picard CollectInsertSizeMetrics 2 | description: | 3 | Collect metrics on insert size of paired end reads with picard tools. 4 | authors: 5 | - Johannes Köster 6 | input: 7 | - bam file 8 | output: 9 | - txt: textual representation of metrics 10 | - pdf: insert size histogram 11 | -------------------------------------------------------------------------------- /wrappers/samtools/faidx/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Michael Chambers" 2 | __copyright__ = "Copyright 2019, Michael Chambers" 3 | __email__ = "greenkidneybean@gmail.com" 4 | __license__ = "MIT" 5 | 6 | 7 | from snakemake.shell import shell 8 | 9 | 10 | shell("samtools faidx {snakemake.params} {snakemake.input[0]} > {snakemake.output[0]}") 11 | -------------------------------------------------------------------------------- /wrappers/samtools/idxstats/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule samtools_idxstats: 2 | input: 3 | bam="mapped/{sample}.bam", 4 | idx="mapped/{sample}.bam.bai" 5 | output: 6 | "mapped/{sample}.bam.idxstats" 7 | log: 8 | "logs/samtools/idxstats/{sample}.log" 9 | wrapper: 10 | "master/bio/samtools/idxstats" 11 | -------------------------------------------------------------------------------- /wrappers/multiqc/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule multiqc: 2 | input: 3 | expand("samtools_stats/{sample}.txt", sample=["a", "b"]) 4 | output: 5 | "qc/multiqc.html" 6 | params: 7 | "" # Optional: extra parameters for multiqc. 8 | log: 9 | "logs/multiqc.log" 10 | wrapper: 11 | "master/bio/multiqc" 12 | -------------------------------------------------------------------------------- /wrappers/wham/wrapper.py: -------------------------------------------------------------------------------- 1 | from snakemake.shell import shell 2 | 3 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 4 | 5 | shell( 6 | "(whamg " 7 | "-x {snakemake.threads} " 8 | "-a {snakemake.input.fasta} " 9 | "-f {snakemake.input.bam} " 10 | "-c {snakemake.params.include_chroms} > {snakemake.output}) {log} " 11 | ) 12 | -------------------------------------------------------------------------------- /wrappers/bwa/aln/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule bwa_aln: 2 | input: 3 | "reads/{sample}.{pair}.fastq" 4 | output: 5 | "sai/{sample}.{pair}.sai" 6 | params: 7 | index="genome", 8 | extra="" 9 | log: 10 | "logs/bwa_aln/{sample}.{pair}.log" 11 | threads: 8 12 | wrapper: 13 | "master/bio/bwa/aln" 14 | -------------------------------------------------------------------------------- /wrappers/samtools/view/test/a.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:xx LN:20 2 | a1 99 xx 1 1 10M = 11 20 AAAAAAAAAA ********** 3 | b1 99 xx 1 1 10M = 11 20 AAAAAAAAAA ********** 4 | c1 99 xx 1 1 10M = 11 20 AAAAAAAAAA ********** 5 | a1 147 xx 11 1 10M = 1 -20 TTTTTTTTTT ********** 6 | b1 147 xx 11 1 10M = 1 -20 TTTTTTTTTT ********** 7 | c1 147 xx 11 1 10M = 1 -20 TTTTTTTTTT ********** 8 | -------------------------------------------------------------------------------- /wrappers/samtools/merge/meta.yaml: -------------------------------------------------------------------------------- 1 | name: samtools merge 2 | description: Merge two bam files with samtools. 3 | authors: 4 | - Johannes Köster 5 | input: 6 | - list of bam files to merge 7 | output: 8 | - merged bam file 9 | notes: | 10 | * Samtools -@/--threads takes one integer as input. This is the number of additional threads and not raw threads. 11 | -------------------------------------------------------------------------------- /wrappers/gatk/combinegvcfs/test/genome.dict: -------------------------------------------------------------------------------- 1 | @HD VN:1.5 2 | @SQ SN:ref LN:45 M5:7a66cae8ab14aef8d635bc80649e730b UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta 3 | @SQ SN:ref2 LN:40 M5:1636753510ec27476fdd109a6684680e UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta 4 | -------------------------------------------------------------------------------- /wrappers/gatk/genotypegvcfs/test/genome.dict: -------------------------------------------------------------------------------- 1 | @HD VN:1.5 2 | @SQ SN:ref LN:45 M5:7a66cae8ab14aef8d635bc80649e730b UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta 3 | @SQ SN:ref2 LN:40 M5:1636753510ec27476fdd109a6684680e UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta 4 | -------------------------------------------------------------------------------- /wrappers/gatk/haplotypecaller/test/genome.dict: -------------------------------------------------------------------------------- 1 | @HD VN:1.5 2 | @SQ SN:ref LN:45 M5:7a66cae8ab14aef8d635bc80649e730b UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta 3 | @SQ SN:ref2 LN:40 M5:1636753510ec27476fdd109a6684680e UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta 4 | -------------------------------------------------------------------------------- /wrappers/gatk/mutect/test/genome/genome.dict: -------------------------------------------------------------------------------- 1 | @HD VN:1.5 2 | @SQ SN:ref LN:45 M5:7a66cae8ab14aef8d635bc80649e730b UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta 3 | @SQ SN:ref2 LN:40 M5:1636753510ec27476fdd109a6684680e UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta 4 | -------------------------------------------------------------------------------- /wrappers/gatk/selectvariants/test/genome.dict: -------------------------------------------------------------------------------- 1 | @HD VN:1.5 2 | @SQ SN:ref LN:45 M5:7a66cae8ab14aef8d635bc80649e730b UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta 3 | @SQ SN:ref2 LN:40 M5:1636753510ec27476fdd109a6684680e UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta 4 | -------------------------------------------------------------------------------- /wrappers/picard/mergesamfiles/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule merge_bams: 2 | input: 3 | expand("mapped/{sample}.bam", sample=["a", "b"]) 4 | output: 5 | "merged.bam" 6 | log: 7 | "logs/picard_mergesamfiles.log" 8 | params: 9 | "VALIDATION_STRINGENCY=LENIENT" 10 | wrapper: 11 | "master/bio/picard/mergesamfiles" 12 | -------------------------------------------------------------------------------- /wrappers/samtools/fixmate/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule samtools_fixmate: 2 | input: 3 | "mapped/{input}" 4 | output: 5 | "fixed/{input}" 6 | message: 7 | "Fixing mate information in {wildcards.input}" 8 | threads: 9 | 1 10 | params: 11 | extra = "" 12 | wrapper: 13 | "master/bio/samtools/fixmate/" 14 | -------------------------------------------------------------------------------- /wrappers/gatk/baserecalibrator/test/genome.dict: -------------------------------------------------------------------------------- 1 | @HD VN:1.5 2 | @SQ SN:ref LN:45 M5:7a66cae8ab14aef8d635bc80649e730b UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta 3 | @SQ SN:ref2 LN:40 M5:1636753510ec27476fdd109a6684680e UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta 4 | -------------------------------------------------------------------------------- /wrappers/gatk/splitncigarreads/test/genome.dict: -------------------------------------------------------------------------------- 1 | @HD VN:1.5 2 | @SQ SN:ref LN:45 M5:7a66cae8ab14aef8d635bc80649e730b UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta 3 | @SQ SN:ref2 LN:40 M5:1636753510ec27476fdd109a6684680e UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta 4 | -------------------------------------------------------------------------------- /wrappers/gatk/variantfiltration/test/genome.dict: -------------------------------------------------------------------------------- 1 | @HD VN:1.5 2 | @SQ SN:ref LN:45 M5:7a66cae8ab14aef8d635bc80649e730b UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta 3 | @SQ SN:ref2 LN:40 M5:1636753510ec27476fdd109a6684680e UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta 4 | -------------------------------------------------------------------------------- /wrappers/gatk3/haplotypecaller/test/genome.dict: -------------------------------------------------------------------------------- 1 | @HD VN:1.5 2 | @SQ SN:ref LN:45 M5:7a66cae8ab14aef8d635bc80649e730b UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta 3 | @SQ SN:ref2 LN:40 M5:1636753510ec27476fdd109a6684680e UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta 4 | -------------------------------------------------------------------------------- /wrappers/picard/createsequencedictionary/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule create_dict: 2 | input: 3 | "genome.fasta" 4 | output: 5 | "genome.dict" 6 | log: 7 | "logs/picard/create_dict.log" 8 | params: 9 | extra="" # optional: extra arguments for picard. 10 | wrapper: 11 | "master/bio/picard/createsequencedictionary" 12 | -------------------------------------------------------------------------------- /wrappers/picard/revertsam/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule revert_bam: 2 | input: 3 | "mapped/{sample}.bam" 4 | output: 5 | "revert/{sample}.bam" 6 | log: 7 | "logs/picard/revert_sam/{sample}.log" 8 | params: 9 | extra="SANITIZE=true" # optional: Extra arguments for picard. 10 | wrapper: 11 | "master/bio/picard/revertsam" 12 | -------------------------------------------------------------------------------- /wrappers/reference/ensembl-annotation/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule get_annotation: 2 | output: 3 | "refs/annotation.gtf" 4 | params: 5 | species="homo_sapiens", 6 | release="98", 7 | build="GRCh38", 8 | fmt="gtf" 9 | log: 10 | "logs/get_annotation.log" 11 | wrapper: 12 | "master/bio/reference/ensembl-annotation" 13 | -------------------------------------------------------------------------------- /wrappers/bcftools/index/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Johannes Köster" 2 | __copyright__ = "Copyright 2016, Johannes Köster" 3 | __email__ = "koester@jimmy.harvard.edu" 4 | __license__ = "MIT" 5 | 6 | 7 | from snakemake.shell import shell 8 | 9 | ## Extract arguments 10 | extra = snakemake.params.get("extra", "") 11 | 12 | shell("bcftools index" " {extra}" " {snakemake.input[0]}") 13 | -------------------------------------------------------------------------------- /wrappers/gatk/filtermutectcalls/wrapper.py: -------------------------------------------------------------------------------- 1 | from snakemake.shell import shell 2 | 3 | extra = snakemake.params.get("extra", "") 4 | 5 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 6 | 7 | shell( 8 | "gatk FilterMutectCalls " 9 | "-R {snakemake.input.fasta} -V {snakemake.input.vcf} " 10 | "{extra} " 11 | "-O {snakemake.output.vcf} " 12 | "{log}" 13 | ) -------------------------------------------------------------------------------- /wrappers/mity/call/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | dependencies: 5 | - python > 3.7 6 | - numpy==1.16.4 7 | - pandas==0.24.2 8 | - pysam==0.15.3 9 | - python-dateutil==2.8.0 10 | - pytz==2019.1 11 | - pyvcf==0.6.8 12 | - scipy==1.3.2 13 | - six==1.12.0 14 | - xlsxwriter==1.1.8 15 | - freebayes ==1.3.1 16 | - gsort==0.1.4 17 | -------------------------------------------------------------------------------- /wrappers/reference/ensembl-sequence/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule get_genome: 2 | output: 3 | "refs/genome.fasta" 4 | params: 5 | species="saccharomyces_cerevisiae", 6 | datatype="dna", 7 | build="R64-1-1", 8 | release="98" 9 | log: 10 | "logs/get_genome.log" 11 | wrapper: 12 | "master/bio/reference/ensembl-sequence" 13 | -------------------------------------------------------------------------------- /wrappers/samtools/idxstats/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Antonie Vietor" 2 | __copyright__ = "Copyright 2020, Antonie Vietor" 3 | __email__ = "antonie.v@gmx.de" 4 | __license__ = "MIT" 5 | 6 | 7 | from snakemake.shell import shell 8 | 9 | log = snakemake.log_fmt_shell(stdout=False, stderr=True) 10 | 11 | shell("samtools idxstats {snakemake.input.bam} > {snakemake.output[0]} {log}") 12 | -------------------------------------------------------------------------------- /envs/cre.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - conda-forge 3 | - bioconda 4 | - defaults 5 | - r 6 | dependencies: 7 | - gemini =0.30.2 8 | - vt =2015.11.10 9 | - bcftools =1.9 10 | - bedtools =2.29.2 11 | - gatk4 =4.1.6.0 12 | - gatk =3.8 13 | - tabix =0.2.6 14 | - r =3.6.0 15 | - r-stringr =1.4.0 16 | - r-data.table =1.12.2 17 | - r-dplyr =0.8.0.1 18 | - r-plyr =1.8.4 19 | -------------------------------------------------------------------------------- /wrappers/samtools/sort/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule samtools_sort: 2 | input: 3 | "mapped/{sample}.bam" 4 | output: 5 | "mapped/{sample}.sorted.bam" 6 | params: 7 | "-m 4G" 8 | threads: # Samtools takes additional threads through its option -@ 9 | 8 # This value - 1 will be sent to -@. 10 | wrapper: 11 | "master/bio/samtools/sort" 12 | -------------------------------------------------------------------------------- /wrappers/vep/test/fake_KJ660346.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FORMAT= 3 | ##contig= 4 | ##reference=http://www.ncbi.nlm.nih.gov/nuccore/KJ660346.1 5 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT fake_KJ660346 6 | KJ660346 3116 . C T . . . GT 1 7 | KJ660346 10743 . T G . . . GT 1 8 | KJ660346 15660 . C A . . . GT 1 9 | -------------------------------------------------------------------------------- /wrappers/vt/test/fake_KJ660346.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FORMAT= 3 | ##contig= 4 | ##reference=http://www.ncbi.nlm.nih.gov/nuccore/KJ660346.1 5 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT fake_KJ660346 6 | KJ660346 3116 . C T . . . GT 1 7 | KJ660346 10743 . T G . . . GT 1 8 | KJ660346 15660 . C A . . . GT 1 9 | -------------------------------------------------------------------------------- /benchmark_cheo_ri.tsv: -------------------------------------------------------------------------------- 1 | family sample pipeline baseline_vcf high_conf_bed 2 | HG001 NA12878 wes /srv/shared/data/dccdipg/Common/rtg-tools/NISTv3.3.2/HG001_truth.vcf.gz /srv/shared/data/dccdipg/Common/rtg-tools/NISTv3.3.2/HG001_exome_truth.bed 3 | HG001 NA12878 wgs /srv/shared/data/dccdipg/Common/rtg-tools/NISTv3.3.2/HG001_truth.vcf.gz /srv/shared/data/dccdipg/Common/rtg-tools/NISTv3.3.2/HG001_truth.bed 4 | -------------------------------------------------------------------------------- /wrappers/mity/normalise/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | dependencies: 5 | - python > 3.7 6 | - numpy==1.16.4 7 | - pandas==0.24.2 8 | - pysam==0.15.3 9 | - python-dateutil==2.8.0 10 | - pytz==2019.1 11 | - pyvcf==0.6.8 12 | - scipy==1.3.2 13 | - six==1.12.0 14 | - xlsxwriter==1.1.8 15 | - freebayes ==1.3.1 16 | - gsort==0.1.4 17 | - vt -------------------------------------------------------------------------------- /wrappers/picard/addorreplacereadgroups/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule replace_rg: 2 | input: 3 | "mapped/{sample}.bam" 4 | output: 5 | "fixed-rg/{sample}.bam" 6 | log: 7 | "logs/picard/replace_rg/{sample}.log" 8 | params: 9 | "RGLB=lib1 RGPL=illumina RGPU={sample} RGSM={sample}" 10 | wrapper: 11 | "master/bio/picard/addorreplacereadgroups" 12 | -------------------------------------------------------------------------------- /wrappers/platypus/meta.yaml: -------------------------------------------------------------------------------- 1 | name: Platypus variant caller 2 | description: | 3 | Run platypus variant caller for single/multiple bams and regions (optional) 4 | authors: 5 | - Aarthi Mohan 6 | input: 7 | - bam file(s) 8 | - region file (optional) 9 | output: 10 | - VCF file 11 | notes: | 12 | * For full usage see, https://github.com/andyrimmer/Platypus/blob/master/misc/README.txt 13 | -------------------------------------------------------------------------------- /wrappers/snpeff/test/fake_KJ660346.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FORMAT= 3 | ##contig= 4 | ##reference=http://www.ncbi.nlm.nih.gov/nuccore/KJ660346.1 5 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT fake_KJ660346 6 | KJ660346 3116 . C T . . . GT 1 7 | KJ660346 10743 . T G . . . GT 1 8 | KJ660346 15660 . C A . . . GT 1 9 | -------------------------------------------------------------------------------- /wrappers/vcf2db/test/fake_KJ660346.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FORMAT= 3 | ##contig= 4 | ##reference=http://www.ncbi.nlm.nih.gov/nuccore/KJ660346.1 5 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT fake_KJ660346 6 | KJ660346 3116 . C T . . . GT 1 7 | KJ660346 10743 . T G . . . GT 1 8 | KJ660346 15660 . C A . . . GT 1 9 | -------------------------------------------------------------------------------- /wrappers/vcfanno/test/fake_KJ660346.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FORMAT= 3 | ##contig= 4 | ##reference=http://www.ncbi.nlm.nih.gov/nuccore/KJ660346.1 5 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT fake_KJ660346 6 | KJ660346 3116 . C T . . . GT 1 7 | KJ660346 10743 . T G . . . GT 1 8 | KJ660346 15660 . C A . . . GT 1 9 | -------------------------------------------------------------------------------- /wrappers/bedtools/coveragebed/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule coverageBed: 2 | input: 3 | a="bed/{sample}.bed", 4 | b="mapped/{sample}.bam" 5 | output: 6 | "stats/{sample}.cov" 7 | log: 8 | "logs/coveragebed/{sample}.log" 9 | params: 10 | extra="" # optional parameters 11 | threads: 8 12 | wrapper: 13 | "master/bio/bedtools/coveragebed" 14 | -------------------------------------------------------------------------------- /wrappers/picard/markduplicates/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule mark_duplicates: 2 | input: 3 | "mapped/{sample}.bam" 4 | output: 5 | bam="dedup/{sample}.bam", 6 | metrics="dedup/{sample}.metrics.txt" 7 | log: 8 | "logs/picard/dedup/{sample}.log" 9 | params: 10 | "REMOVE_DUPLICATES=true" 11 | wrapper: 12 | "master/bio/picard/markduplicates" 13 | -------------------------------------------------------------------------------- /wrappers/samtools/depth/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule samtools_depth: 2 | input: 3 | bams=["mapped/A.bam", "mapped/B.bam"], 4 | bed="regionToCalcDepth.bed", # optional 5 | output: 6 | "depth.txt" 7 | params: 8 | # optional bed file passed to -b 9 | extra="" # optional additional parameters as string 10 | wrapper: 11 | "master/bio/samtools/depth" 12 | -------------------------------------------------------------------------------- /wrappers/mity/report/environment.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | dependencies: 5 | - python > 3.7 6 | - numpy==1.16.4 7 | - pandas==0.24.2 8 | - pysam==0.15.3 9 | - python-dateutil==2.8.0 10 | - pytz==2019.1 11 | - pyvcf==0.6.8 12 | - scipy==1.3.2 13 | - six==1.12.0 14 | - xlsxwriter==1.1.8 15 | - freebayes ==1.3.1 16 | - gsort==0.1.4 17 | - vcfanno==0.3.2 18 | -------------------------------------------------------------------------------- /wrappers/vcf2db/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule vcf2db: 2 | input: 3 | "{sample}.vcf", # (vcf, bcf, or vcf.gz) 4 | output: 5 | db="annotated/gemini.db", 6 | log: 7 | "logs/vcf2db/vcf2db.log" 8 | params: 9 | ped=config["annotation"]["vcf2db"]["ped"], 10 | threads: 1 11 | resources: 12 | mem_mb = 10000 13 | wrapper: 14 | "master/bio/vcf2db" 15 | -------------------------------------------------------------------------------- /wrappers/picard/addorreplacereadgroups/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Johannes Köster" 2 | __copyright__ = "Copyright 2016, Johannes Köster" 3 | __email__ = "koester@jimmy.harvard.edu" 4 | __license__ = "MIT" 5 | 6 | 7 | from snakemake.shell import shell 8 | 9 | 10 | shell( 11 | "picard AddOrReplaceReadGroups {snakemake.params} I={snakemake.input} " 12 | "O={snakemake.output} &> {snakemake.log}" 13 | ) 14 | -------------------------------------------------------------------------------- /wrappers/bedtools/merge/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule bedtools_merge: 2 | input: 3 | "A.bed" 4 | output: 5 | "A.merged.bed" 6 | params: 7 | ## Add optional parameters 8 | extra="-c 1 -o count" ## In this example, we want to count how many input lines we merged per output line 9 | log: 10 | "logs/merge/A.log" 11 | wrapper: 12 | "master/bio/bedtools/merge" 13 | -------------------------------------------------------------------------------- /wrappers/gatk/mutect/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule mutect2: 2 | input: 3 | fasta = "genome/genome.fasta", 4 | map = "mapped/{sample}.bam" 5 | output: 6 | vcf = "variant/{sample}.vcf" 7 | message: 8 | "Testing Mutect2 with {wildcards.sample}" 9 | threads: 10 | 1 11 | log: 12 | "logs/mutect_{sample}.log" 13 | wrapper: 14 | "master/bio/gatk/mutect" 15 | -------------------------------------------------------------------------------- /wrappers/picard/sortsam/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule sort_bam: 2 | input: 3 | "mapped/{sample}.bam" 4 | output: 5 | "sorted/{sample}.bam" 6 | log: 7 | "logs/picard/sort_sam/{sample}.log" 8 | params: 9 | sort_order="coordinate", 10 | extra="VALIDATION_STRINGENCY=LENIENT" # optional: Extra arguments for picard. 11 | wrapper: 12 | "master/bio/picard/sortsam" 13 | -------------------------------------------------------------------------------- /wrappers/gatk/combinegvcfs/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule genotype_gvcfs: 2 | input: 3 | gvcfs=["calls/a.g.vcf", "calls/b.g.vcf"], 4 | ref="genome.fasta" 5 | output: 6 | gvcf="calls/all.g.vcf", 7 | log: 8 | "logs/gatk/combinegvcfs.log" 9 | params: 10 | extra="", # optional 11 | java_opts="", # optional 12 | wrapper: 13 | "master/bio/gatk/combinegvcfs" 14 | -------------------------------------------------------------------------------- /wrappers/picard/samtofastq/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule bam_to_fastq: 2 | input: 3 | "mapped/{sample}.bam" 4 | output: 5 | fastq1="reads/{sample}.R1.fastq", 6 | fastq2="reads/{sample}.R2.fastq" 7 | log: 8 | "logs/picard/sam_to_fastq/{sample}.log" 9 | params: 10 | extra="" # optional: Extra arguments for picard. 11 | wrapper: 12 | "master/bio/picard/samtofastq" 13 | -------------------------------------------------------------------------------- /wrappers/samtools/merge/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule samtools_merge: 2 | input: 3 | ["mapped/A.bam", "mapped/B.bam"] 4 | output: 5 | "merged.bam" 6 | params: 7 | "" # optional additional parameters as string 8 | threads: # Samtools takes additional threads through its option -@ 9 | 8 # This value - 1 will be sent to -@ 10 | wrapper: 11 | "master/bio/samtools/merge" 12 | -------------------------------------------------------------------------------- /wrappers/fastq_screen/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule fastq_screen: 2 | input: 3 | "samples/{sample}.fastq.gz" 4 | output: 5 | txt="qc/{sample}.fastq_screen.txt", 6 | png="qc/{sample}.fastq_screen.png" 7 | params: 8 | fastq_screen_config=fastq_screen_config, 9 | subset=100000, 10 | aligner='bowtie2' 11 | threads: 8 12 | wrapper: 13 | "master/bio/fastq_screen" 14 | -------------------------------------------------------------------------------- /wrappers/gatk/splitncigarreads/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule splitncigarreads: 2 | input: 3 | bam="mapped/{sample}.bam", 4 | ref="genome.fasta" 5 | output: 6 | "split/{sample}.bam" 7 | log: 8 | "logs/gatk/splitNCIGARreads/{sample}.log" 9 | params: 10 | extra="", # optional 11 | java_opts="", # optional 12 | wrapper: 13 | "master/bio/gatk/splitncigarreads" 14 | -------------------------------------------------------------------------------- /wrappers/bwa/index/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule bwa_index: 2 | input: 3 | "{genome}.fasta" 4 | output: 5 | "{genome}.amb", 6 | "{genome}.ann", 7 | "{genome}.bwt", 8 | "{genome}.pac", 9 | "{genome}.sa" 10 | log: 11 | "logs/bwa_index/{genome}.log" 12 | params: 13 | prefix="{genome}", 14 | algorithm="bwtsw" 15 | wrapper: 16 | "master/bio/bwa/index" -------------------------------------------------------------------------------- /wrappers/samtools/mpileup/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule mpilup: 2 | input: 3 | # single or list of bam files 4 | bam="mapped/{sample}.bam", 5 | reference_genome="genome.fasta" 6 | output: 7 | "mpileup/{sample}.mpileup.gz" 8 | log: 9 | "logs/samtools/mpileup/{sample}.log" 10 | params: 11 | extra="-d 10000", # optional 12 | wrapper: 13 | "master/bio/samtools/mpileup" 14 | -------------------------------------------------------------------------------- /wrappers/tabix/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Johannes Köster" 2 | __copyright__ = "Copyright 2016, Johannes Köster" 3 | __email__ = "koester@jimmy.harvard.edu" 4 | __license__ = "MIT" 5 | 6 | 7 | from snakemake.shell import shell 8 | 9 | log = snakemake.log_fmt_shell(stdout=False, stderr=True) 10 | params = "" 11 | if {snakemake.params}: 12 | params = {snakemake.params} 13 | 14 | 15 | shell("tabix {params} {snakemake.input} {log}") 16 | -------------------------------------------------------------------------------- /wrappers/gatk/genotypegvcfs/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule genotype_gvcfs: 2 | input: 3 | gvcf="calls/all.g.vcf", # combined gvcf over multiple samples 4 | ref="genome.fasta" 5 | output: 6 | vcf="calls/all.vcf", 7 | log: 8 | "logs/gatk/genotypegvcfs.log" 9 | params: 10 | extra="", # optional 11 | java_opts="", # optional 12 | wrapper: 13 | "master/bio/gatk/genotypegvcfs" 14 | -------------------------------------------------------------------------------- /wrappers/samtools/stats/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule samtools_stats: 2 | input: 3 | "mapped/{sample}.bam" 4 | output: 5 | "samtools_stats/{sample}.txt" 6 | params: 7 | extra="", # Optional: extra arguments. 8 | region="xx:1000000-2000000" # Optional: region string. 9 | log: 10 | "logs/samtools_stats/{sample}.log" 11 | wrapper: 12 | "master/bio/samtools/stats" 13 | -------------------------------------------------------------------------------- /wrappers/fastqc/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule fastqc: 2 | input: 3 | "reads/{sample}.fastq" 4 | output: 5 | html="qc/fastqc/{sample}.html", 6 | zip="qc/fastqc/{sample}_fastqc.zip" # the suffix _fastqc.zip is necessary for multiqc to find the file. If not using multiqc, you are free to choose an arbitrary filename 7 | params: "" 8 | log: 9 | "logs/fastqc/{sample}.log" 10 | wrapper: 11 | "master/bio/fastqc" 12 | -------------------------------------------------------------------------------- /wrappers/gatk/selectvariants/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule gatk_select: 2 | input: 3 | vcf="calls/all.vcf", 4 | ref="genome.fasta", 5 | output: 6 | vcf="calls/snvs.vcf" 7 | log: 8 | "logs/gatk/select/snvs.log" 9 | params: 10 | extra="--select-type-to-include SNP", # optional filter arguments, see GATK docs 11 | java_opts="", # optional 12 | wrapper: 13 | "master/bio/gatk/selectvariants" 14 | -------------------------------------------------------------------------------- /wrappers/bedtools/intersect/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule bedtools_merge: 2 | input: 3 | left="A.bed", 4 | right="B.bed" 5 | output: 6 | "A_B.intersected.bed" 7 | params: 8 | ## Add optional parameters 9 | extra="-wa -wb" ## In this example, we want to write original entries in A and B for each overlap. 10 | log: 11 | "logs/intersect/A_B.log" 12 | wrapper: 13 | "master/bio/bedtools/intersect" 14 | -------------------------------------------------------------------------------- /wrappers/gatk/baserecalibrator/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule gatk_bqsr: 2 | input: 3 | bam="mapped/{sample}.bam", 4 | ref="genome.fasta", 5 | known="dbsnp.vcf.gz" # optional known sites 6 | output: 7 | bam="recal/{sample}.bam" 8 | log: 9 | "logs/gatk/bqsr/{sample}.log" 10 | params: 11 | extra="", # optional 12 | java_opts="", # optional 13 | wrapper: 14 | "master/bio/gatk/baserecalibrator" 15 | -------------------------------------------------------------------------------- /wrappers/gatk3/baserecalibrator/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule baserecalibrator: 2 | input: 3 | bam="mapped/{sample}.bam", 4 | ref="genome.fasta", 5 | known="dbsnp.vcf.gz" 6 | output: 7 | "{sample}.recal_data_table" 8 | log: 9 | "logs/gatk3/bqsr/{sample}.log" 10 | params: 11 | extra="" # optional 12 | resources: 13 | mem_mb = 1024 14 | threads: 16 15 | wrapper: 16 | "bio/gatk/baserecalibrator" 17 | -------------------------------------------------------------------------------- /benchmark_hpf.tsv: -------------------------------------------------------------------------------- 1 | family sample pipeline baseline_vcf high_conf_bed 2 | HG001 NA12878 wes /hpf/largeprojects/ccmbio/ccmmarvin_shared/validation/benchmarking/NISTv3.3.2/HG001_truth.vcf.gz /hpf/largeprojects/ccmbio/ccmmarvin_shared/validation/benchmarking/NISTv3.3.2/HG001_exome_truth.bed 3 | HG001 NA12878 wgs /hpf/largeprojects/ccmbio/ccmmarvin_shared/validation/benchmarking/NISTv3.3.2/HG001_truth.vcf.gz /hpf/largeprojects/ccmbio/ccmmarvin_shared/validation/benchmarking/NISTv3.3.2/HG001_truth.bed -------------------------------------------------------------------------------- /wrappers/gatk3/printreads/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule printreads: 2 | input: 3 | bam="mapped/{sample}.bam", 4 | ref="genome.fasta", 5 | recal_data="{sample}.recal_data_table" 6 | output: 7 | "alignment/{sample}.bqsr.bam" 8 | log: 9 | "logs/gatk/bqsr/{sample}..log" 10 | params: 11 | extra="" # optional 12 | resources: 13 | mem_mb = 1024 14 | threads: 16 15 | wrapper: 16 | "bio/gatk3/printreads" 17 | -------------------------------------------------------------------------------- /wrappers/igv-reports/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule igv_report: 2 | input: 3 | fasta="minigenome.fa", 4 | vcf="variants.vcf", 5 | # any number of additional optional tracks, see igv-reports manual 6 | tracks=["alignments.bam"] 7 | output: 8 | "igv-report.html" 9 | params: 10 | extra="" # optional params, see igv-reports manual 11 | log: 12 | "logs/igv-report.log" 13 | wrapper: 14 | "master/bio/igv-reports" 15 | -------------------------------------------------------------------------------- /wrappers/picard/collecttargetedpcrmetrics/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule CollectTargetedPcrMetrics: 2 | input: 3 | bam="mapped/{sample}.bam", 4 | amplicon_intervals="amplicon.list", 5 | target_intervals="target.list" 6 | output: 7 | "stats/{sample}.pcr.txt" 8 | log: 9 | "logs/picard/collecttargetedpcrmetrics/{sample}.log" 10 | params: 11 | extra="" 12 | wrapper: 13 | "master/bio/picard/collecttargetedpcrmetrics" 14 | -------------------------------------------------------------------------------- /wrappers/vcfanno/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule vcfanno: 2 | input: 3 | "{sample}.vcf", # (vcf, bcf, or vcf.gz) 4 | output: 5 | calls="vcfanno/{sample}.vcf", # annotated calls (vcf, bcf, or vcf.gz) 6 | log: 7 | "logs/vcfanno/{sample}.log" 8 | params: 9 | lua_script=config["annotation"]["vcfanno"]["lua_script"], 10 | conf=config["annotation"]["vcfanno"]["conf"], 11 | threads="5", 12 | wrapper: 13 | "master/bio/vcfanno" 14 | -------------------------------------------------------------------------------- /sample_info.tsv: -------------------------------------------------------------------------------- 1 | familyID sample fq1 fq2 bam 2 | HG001 NA12878 /hpf/largeprojects/ccm_dccforge/dccdipg/Common/NA12878/NA12878.bam_1.fq.gz /hpf/largeprojects/ccm_dccforge/dccdipg/Common/NA12878/NA12878.bam_2.fq.gz 3 | 1159R CH0531 /hpf/largeprojects/ccm_dccforge/dccdipg/c4r_wgs/2019/1159R/1159R_CH0531.bam 4 | 1159R CH0879 /hpf/largeprojects/ccm_dccforge/dccdipg/c4r_wgs/2019/1159R/1159R_CH0879.bam 5 | 1159R CH0880 /hpf/largeprojects/ccm_dccforge/dccdipg/c4r_wgs/2019/1159R/1159R_CH0880.bam 6 | -------------------------------------------------------------------------------- /wrappers/mity/call/wrapper.py: -------------------------------------------------------------------------------- 1 | from snakemake.shell import shell 2 | 3 | log = snakemake.log_fmt_shell(stdout=True, stderr=True, append=True) 4 | 5 | family = snakemake.wildcards.family 6 | outdir = snakemake.params.outdir 7 | tool = snakemake.params.tool 8 | pythonpath = tool.replace("bin", "") 9 | 10 | python = " export PYTHONPATH={pythonpath}; " 11 | mity = " {tool}/mity call --prefix {family} --output-dir {outdir} -k {snakemake.input.bam} " 12 | shell("(" + python + mity + ") {log}") 13 | -------------------------------------------------------------------------------- /wrappers/peddy/wrapper.py: -------------------------------------------------------------------------------- 1 | from snakemake.shell import shell 2 | import os.path 3 | from os import path 4 | 5 | 6 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 7 | extra = snakemake.params.get("extra", "") 8 | 9 | family = snakemake.wildcards.family 10 | dir = os.path.dirname(snakemake.output[0]) 11 | prefix = path.join(dir, family) # qc/peddy/412 12 | 13 | shell( 14 | "peddy {snakemake.params} --prefix {prefix} {snakemake.input.vcf} {snakemake.input.ped} {log} " 15 | ) 16 | -------------------------------------------------------------------------------- /wrappers/reference/ensembl-variation/test/with_fai.smk: -------------------------------------------------------------------------------- 1 | rule get_variation_with_contig_lengths: 2 | input: 3 | fai="refs/genome.fasta.fai" 4 | output: 5 | vcf="refs/variation.vcf.gz" 6 | params: 7 | species="saccharomyces_cerevisiae", 8 | release="98", 9 | type="all" # one of "all", "somatic", "structural_variation" 10 | log: 11 | "logs/get_variation.log" 12 | wrapper: 13 | "master/bio/reference/ensembl-variation" 14 | -------------------------------------------------------------------------------- /get_dependency.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | #usage: sh get_dependency.sh 4 | #generate this once; write a rule to copy the output file 5 | #output=dependencies_; run this from crg2 repo path 6 | 7 | 8 | d=`date +%m-%d-%Y`; 9 | if [ -z $2 ]; then 10 | out="programs.${d}.txt"; 11 | else 12 | out=$2; 13 | fi; 14 | for i in `find $1 -name "environment.yaml"`; do grep "==" $i | awk '{ split($3,a,"=="); print $2,a[2];}' >> $out; done; 15 | cat $out | sort -k1,1 -k2,2 | uniq >> temp && mv temp $out -------------------------------------------------------------------------------- /wrappers/gatk/variantfiltration/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule gatk_filter: 2 | input: 3 | vcf="calls/snvs.vcf", 4 | ref="genome.fasta", 5 | output: 6 | vcf="calls/snvs.filtered.vcf" 7 | log: 8 | "logs/gatk/filter/snvs.log" 9 | params: 10 | filters={"myfilter": "AB < 0.2 || MQ0 > 50"}, 11 | extra="", # optional arguments, see GATK docs 12 | java_opts="", # optional 13 | wrapper: 14 | "master/bio/gatk/variantfiltration" 15 | -------------------------------------------------------------------------------- /rules/snpeff.smk: -------------------------------------------------------------------------------- 1 | rule snpeff: 2 | input: 3 | "filtered/all.vcf.gz", 4 | output: 5 | calls=report("annotated/all.vcf.gz", caption="../report/vcf.rst", category="Calls"), 6 | csvstats="snpeff/all.csv", 7 | stats="snpeff/stats.csv", 8 | log: 9 | "logs/snpeff.log", 10 | params: 11 | reference=config["ref"]["name"], 12 | extra="-Xmx6g", 13 | data_dir=config["annotation"]["snpeff"]["dataDir"], 14 | wrapper: 15 | get_wrapper_path("snpeff") 16 | -------------------------------------------------------------------------------- /slurm_profile/config.yaml: -------------------------------------------------------------------------------- 1 | restart-times: 0 2 | jobscript: "slurm-jobscript.sh" 3 | cluster: "slurm-submit.py" 4 | cluster-status: "slurm-status.py" 5 | cluster-config: "slurm-config.yaml" 6 | max-jobs-per-second: 1 7 | max-status-checks-per-second: 1 8 | cores: 64 9 | local-cores: 1 10 | resources: [cpus=64] 11 | rerun-incomplete: true # recommended for cluster submissions 12 | keep-going: false 13 | notemp: false 14 | immediate-submit: false 15 | latency-wait: 60 16 | verbose: true 17 | printshellcmds: true 18 | -------------------------------------------------------------------------------- /wrappers/bedtools/merge/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Jan Forster" 2 | __copyright__ = "Copyright 2019, Jan Forster" 3 | __email__ = "j.forster@dkfz.de" 4 | __license__ = "MIT" 5 | 6 | from snakemake.shell import shell 7 | 8 | ## Extract arguments 9 | extra = snakemake.params.get("extra", "") 10 | 11 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 12 | 13 | shell( 14 | "( bedtools merge" 15 | " {extra}" 16 | " -i {snakemake.input}" 17 | " > {snakemake.output})" 18 | " {log}" 19 | ) 20 | -------------------------------------------------------------------------------- /wrappers/bedtools/slop/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule bedtools_merge: 2 | input: 3 | "A.bed" 4 | output: 5 | "A.slop.bed" 6 | params: 7 | ## Genome file, tab-seperated file defining the length of every contig 8 | genome="genome.txt", 9 | ## Add optional parameters 10 | extra = "-b 10" ## in this example, we want to increase the feature by 10 bases to both sides 11 | log: 12 | "logs/slop/A.log" 13 | wrapper: 14 | "master/bio/bedtools/slop" 15 | -------------------------------------------------------------------------------- /wrappers/gatk/haplotypecaller/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule haplotype_caller: 2 | input: 3 | # single or list of bam files 4 | bam="mapped/{sample}.bam", 5 | ref="genome.fasta" 6 | # known="dbsnp.vcf" # optional 7 | output: 8 | gvcf="calls/{sample}.g.vcf", 9 | log: 10 | "logs/gatk/haplotypecaller/{sample}.log" 11 | params: 12 | extra="", # optional 13 | java_opts="", # optional 14 | wrapper: 15 | "master/bio/gatk/haplotypecaller" 16 | -------------------------------------------------------------------------------- /wrappers/gatk3/haplotypecaller/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule haplotype_caller: 2 | input: 3 | # single or list of bam files 4 | bam="mapped/{sample}.bam", 5 | ref="genome.fasta" 6 | # known="dbsnp.vcf" # optional 7 | output: 8 | gvcf="calls/{sample}.g.vcf", 9 | log: 10 | "logs/gatk/haplotypecaller/{sample}.log" 11 | params: 12 | extra="", # optional 13 | java_opts="", # optional 14 | wrapper: 15 | "master/bio/gatk/haplotypecaller" 16 | -------------------------------------------------------------------------------- /wrappers/picard/collectinsertsizemetrics/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Johannes Köster" 2 | __copyright__ = "Copyright 2016, Johannes Köster" 3 | __email__ = "johannes.koester@protonmail.com" 4 | __license__ = "MIT" 5 | 6 | 7 | from snakemake.shell import shell 8 | 9 | 10 | log = snakemake.log_fmt_shell() 11 | 12 | 13 | shell( 14 | "picard CollectInsertSizeMetrics {snakemake.params} " 15 | "INPUT={snakemake.input} OUTPUT={snakemake.output.txt} " 16 | "HISTOGRAM_FILE={snakemake.output.pdf} {log}" 17 | ) 18 | -------------------------------------------------------------------------------- /wrappers/EH/wrapper.py: -------------------------------------------------------------------------------- 1 | from snakemake.shell import shell 2 | import os 3 | 4 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 5 | prefix = os.path.splitext(snakemake.output.json)[0].split(".") 6 | 7 | 8 | shell( 9 | "sex={snakemake.params.sex} && " 10 | "( ExpansionHunter" 11 | " --reference {snakemake.params.ref}" 12 | " --reads {snakemake.input.bam}" 13 | " --output-prefix {prefix}" 14 | " --variant-catalog {snakemake.params.catalog}" 15 | " --sex $sex )" 16 | " {log}" 17 | ) 18 | -------------------------------------------------------------------------------- /wrappers/EHdn/wrapper.py: -------------------------------------------------------------------------------- 1 | from snakemake.shell import shell 2 | import os 3 | 4 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 5 | prefix = os.path.splitext(snakemake.output.json)[0].split(".") 6 | 7 | 8 | shell( 9 | "sex={snakemake.params.sex} && " 10 | "( ExpansionHunter" 11 | " --reference {snakemake.params.ref}" 12 | " --reads {snakemake.input.bam}" 13 | " --output-prefix {prefix}" 14 | " --variant-catalog {snakemake.params.catalog}" 15 | " --sex $sex )" 16 | " {log}" 17 | ) 18 | -------------------------------------------------------------------------------- /wrappers/mosdepth/wrapper.py: -------------------------------------------------------------------------------- 1 | from snakemake.shell import shell 2 | 3 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 4 | 5 | 6 | shell( 7 | "(export MOSDEPTH_Q0=NO_COVERAGE && " 8 | " export MOSDEPTH_Q1=LOW_COVERAGE && " 9 | " export MOSDEPTH_Q2=CALLABLE && " 10 | " mosdepth -n -F 1804 -Q 1 --quantize {snakemake.params.quantiles} --by {snakemake.params.by} {snakemake.params.prefix} {snakemake.input.bam} && " 11 | "zgrep 'CALLABLE' {snakemake.output.qbed} > {snakemake.output.bed}) {log}" 12 | ) 13 | -------------------------------------------------------------------------------- /wrappers/picard/collectalignmentsummarymetrics/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Johannes Köster" 2 | __copyright__ = "Copyright 2016, Johannes Köster" 3 | __email__ = "johannes.koester@protonmail.com" 4 | __license__ = "MIT" 5 | 6 | 7 | from snakemake.shell import shell 8 | 9 | 10 | log = snakemake.log_fmt_shell() 11 | 12 | 13 | shell( 14 | "picard CollectAlignmentSummaryMetrics {snakemake.params} " 15 | "INPUT={snakemake.input.bam} OUTPUT={snakemake.output[0]} " 16 | "REFERENCE_SEQUENCE={snakemake.input.ref} {log}" 17 | ) 18 | -------------------------------------------------------------------------------- /wrappers/samtools/bam2fq/interleaved/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "David Laehnemann, Victoria Sack" 2 | __copyright__ = "Copyright 2018, David Laehnemann, Victoria Sack" 3 | __email__ = "david.laehnemann@hhu.de" 4 | __license__ = "MIT" 5 | 6 | 7 | import os 8 | from snakemake.shell import shell 9 | 10 | 11 | prefix = os.path.splitext(snakemake.output[0])[0] 12 | 13 | shell( 14 | "samtools bam2fq {snakemake.params} " 15 | " -@ {snakemake.threads} " 16 | " {snakemake.input[0]}" 17 | " >{snakemake.output[0]} " 18 | ) 19 | -------------------------------------------------------------------------------- /wrappers/snpeff/test/Snakefile_nostats: -------------------------------------------------------------------------------- 1 | rule snpeff: 2 | input: 3 | "{sample}.vcf", 4 | output: 5 | calls="snpeff_nostats/{sample}.vcf", # the main output file 6 | # if either "genes" or "stats" outputs are provided, both are created 7 | log: 8 | "logs/snpeff_nostats/{sample}.log" 9 | params: 10 | reference="ebola_zaire", # reference name (from `snpeff databases`) 11 | extra="" # optional parameters 12 | wrapper: 13 | "master/bio/snpeff" 14 | -------------------------------------------------------------------------------- /wrappers/bwa/mem-samblaster/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule bwa_mem: 2 | input: 3 | reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"] 4 | output: 5 | bam="mapped/{sample}.bam", 6 | index="mapped/{sample}.bam.bai" 7 | log: 8 | "logs/bwa_mem_sambamba/{sample}.log" 9 | params: 10 | index="genome", 11 | extra=r"-R '@RG\tID:{sample}\tSM:{sample}'", 12 | sort_extra="" # Extra args for sambamba. 13 | threads: 8 14 | wrapper: 15 | "master/bio/bwa/mem-samblaster" 16 | -------------------------------------------------------------------------------- /envs/ehdn-report.yaml: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | dependencies: 5 | - python=3.7.8 6 | - python-docx=0.8.10 7 | - pandas=1.1.2 8 | - numpy=1.19.1 9 | - scipy=1.5.2 10 | - xlsxwriter=1.3.7 11 | - r-base=3.4.1 12 | - r-dbscan=1.1.5 13 | - r-ggplot2=3.1.0 14 | - r-data.table=1.11.4 15 | - r-doSNOW=1.0.20 16 | - r-cowplot=0.9.3 17 | - bioconductor-genomicranges=1.32.7 18 | - bioconductor-genomeinfodb=1.16.0 19 | - bioconductor-genomeinfodbdata=1.1.0 20 | - bioconductor-biostrings=2.48.0 21 | 22 | -------------------------------------------------------------------------------- /wrappers/reference/ensembl-variation/test/refs/genome.fasta.fai: -------------------------------------------------------------------------------- 1 | I 230218 54 60 61 2 | II 813184 234165 60 61 3 | III 316620 1060961 60 61 4 | IV 1531933 1382915 60 61 5 | V 576874 2940435 60 61 6 | VI 270161 3526980 60 61 7 | VII 1090940 3801703 60 61 8 | VIII 562643 4910886 60 61 9 | IX 439888 5482963 60 61 10 | X 745751 5930237 60 61 11 | XI 666816 6688474 60 61 12 | XII 1078177 7366463 60 61 13 | XIII 924431 8462670 60 61 14 | XIV 784333 9402567 60 61 15 | XV 1091291 10200030 60 61 16 | XVI 948066 11309568 60 61 17 | Mito 85779 12273495 60 61 18 | -------------------------------------------------------------------------------- /wrappers/bedtools/slop/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Jan Forster" 2 | __copyright__ = "Copyright 2019, Jan Forster" 3 | __email__ = "j.forster@dkfz.de" 4 | __license__ = "MIT" 5 | 6 | from snakemake.shell import shell 7 | 8 | ## Extract arguments 9 | extra = snakemake.params.get("extra", "") 10 | 11 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 12 | 13 | shell( 14 | "(bedtools slop" 15 | " {extra}" 16 | " -i {snakemake.input[0]}" 17 | " -g {snakemake.params.genome}" 18 | " > {snakemake.output})" 19 | " {log}" 20 | ) 21 | -------------------------------------------------------------------------------- /wrappers/platypus/test/Snakefile: -------------------------------------------------------------------------------- 1 | samples = ["a", "b"] 2 | project = "ab" 3 | 4 | rule platypus: 5 | input: 6 | # single or list of bam files 7 | bam=expand("mapped/{sample}.bam", sample=samples), 8 | bai=expand("mapped/{sample}.bam.bai", sample=samples), 9 | ref="genome.fasta", 10 | regions="regions.bed" #remove or empty quotes if not using regions 11 | output: 12 | "calls/{project}-platypus.vcf" 13 | threads: 8 14 | log: 15 | "logs/platypus/{project}.log" 16 | wrapper: 17 | "file:.." -------------------------------------------------------------------------------- /wrappers/reference/ensembl-variation/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule get_variation: 2 | output: 3 | vcf="refs/variation.vcf.gz" 4 | # optional: add fai to get VCF with annotated contig lengths (as required by GATK) 5 | # fai="refs/genome.fasta.fai" 6 | params: 7 | species="saccharomyces_cerevisiae", 8 | release="98", 9 | type="all" # one of "all", "somatic", "structural_variation" 10 | log: 11 | "logs/get_variation.log" 12 | wrapper: 13 | "master/bio/reference/ensembl-variation" 14 | 15 | 16 | -------------------------------------------------------------------------------- /wrappers/picard/createsequencedictionary/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Johannes Köster" 2 | __copyright__ = "Copyright 2018, Johannes Köster" 3 | __email__ = "johannes.koester@protonmail.com" 4 | __license__ = "MIT" 5 | 6 | 7 | from snakemake.shell import shell 8 | 9 | 10 | extra = snakemake.params.get("extra", "") 11 | log = snakemake.log_fmt_shell(stdout=False, stderr=True) 12 | 13 | shell( 14 | "picard " 15 | "CreateSequenceDictionary " 16 | "{extra} " 17 | "R={snakemake.input[0]} " 18 | "O={snakemake.output[0]} " 19 | "{log}" 20 | ) 21 | -------------------------------------------------------------------------------- /dnaseq.pbs: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | #PBS -l walltime=72:00:00,nodes=1:ppn=4 4 | #PBS -joe . 5 | #PBS -d . 6 | #PBS -l vmem=80g,mem=80g 7 | 8 | if [ -z $pipeline ]; then pipeline=$1; fi; 9 | 10 | if [ $pipeline = "wes" ]; then 11 | SF=~/crg2/cre.Snakefile; 12 | else 13 | SF=~/crg2/Snakefile 14 | fi; 15 | 16 | CP="/hpf/largeprojects/ccm_dccforge/dccdipg/Common/snakemake" 17 | 18 | source /hpf/largeprojects/ccm_dccforge/dccdipg/Common/anaconda3/etc/profile.d/conda.sh 19 | conda activate snakemake 20 | 21 | snakemake --use-conda -s ${SF} --cores 4 --conda-prefix ${CP} 22 | -------------------------------------------------------------------------------- /wrappers/bedtools/intersect/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Jan Forster" 2 | __copyright__ = "Copyright 2019, Jan Forster" 3 | __email__ = "j.forster@dkfz.de" 4 | __license__ = "MIT" 5 | 6 | from snakemake.shell import shell 7 | 8 | ## Extract arguments 9 | extra = snakemake.params.get("extra", "") 10 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 11 | 12 | 13 | shell( 14 | "(bedtools intersect" 15 | " {extra}" 16 | " -a {snakemake.input.left}" 17 | " -b {snakemake.input.right}" 18 | " | bgzip -c > {snakemake.output})" 19 | " {log}" 20 | ) 21 | -------------------------------------------------------------------------------- /wrappers/samtools/depth/wrapper.py: -------------------------------------------------------------------------------- 1 | """Snakemake wrapper for running samtools depth.""" 2 | 3 | __author__ = "Dayne L Filer" 4 | __copyright__ = "Copyright 2020, Dayne L Filer" 5 | __email__ = "dayne.filer@gmail.com" 6 | __license__ = "MIT" 7 | 8 | from snakemake.shell import shell 9 | 10 | params = snakemake.params.get("extra", "") 11 | 12 | # check for optional bed file 13 | bed = snakemake.input.get("bed", "") 14 | if bed: 15 | bed = "-b " + bed 16 | 17 | shell( 18 | "samtools depth {params} {bed} " "-o {snakemake.output[0]} {snakemake.input.bams}" 19 | ) 20 | -------------------------------------------------------------------------------- /wrappers/picard/revertsam/wrapper.py: -------------------------------------------------------------------------------- 1 | """Snakemake wrapper for picard RevertSam.""" 2 | 3 | __author__ = "Patrik Smeds" 4 | __copyright__ = "Copyright 2018, Patrik Smeds" 5 | __email__ = "patrik.smeds@gmail.com" 6 | __license__ = "MIT" 7 | 8 | 9 | from snakemake.shell import shell 10 | 11 | extra = snakemake.params.get("extra", "") 12 | log = snakemake.log_fmt_shell(stdout=False, stderr=True) 13 | 14 | shell( 15 | "picard" 16 | " RevertSam" 17 | " {extra}" 18 | " INPUT={snakemake.input[0]}" 19 | " OUTPUT={snakemake.output[0]}" 20 | " {log}" 21 | ) 22 | -------------------------------------------------------------------------------- /scripts/annotate-caller.sh: -------------------------------------------------------------------------------- 1 | 2 | #!/bin/bash 3 | 4 | read -r -a l <<< $@; 5 | a=($(echo ${l[4]} | awk '{ split($1,x,""); print x[1],x[2],x[3],x[4];}')); 6 | callers=(); 7 | sum=$(IFS=+; echo "$((${a[*]}))") 8 | if [[ ${a[0]} == 1 ]]; then callers+=("gatk-haplotype"); fi; 9 | if [[ ${a[1]} == 1 ]]; then callers+=("samtools"); fi; 10 | if [[ ${a[2]} == 1 ]]; then callers+=("freebayes"); fi; 11 | if [[ ${a[3]} == 1 ]]; then callers+=("platypus"); fi; 12 | callers=$(IFS=","; echo "${callers[*]};"); 13 | echo -e "${l[0]}\t${l[1]}\t${l[2]}\t${l[3]}\t${callers}\t${sum}"; 14 | 15 | -------------------------------------------------------------------------------- /wrappers/gatk/splitncigarreads/meta.yaml: -------------------------------------------------------------------------------- 1 | name: gatk SplitNCigarReads 2 | description: | 3 | Run gatk SplitNCigarReads. 4 | authors: 5 | - Jan Forster 6 | input: 7 | - bam file 8 | output: 9 | - split bam file 10 | notes: | 11 | * The `java_opts` param allows for additional arguments to be passed to the java compiler, e.g. "-Xmx4G" for one, and "-Xmx4G -XX:ParallelGCThreads=10" for two options. 12 | * The `extra` param alllows for additional program arguments. 13 | * For more inforamtion see, https://software.broadinstitute.org/gatk/documentation/article?id=11050 14 | 15 | -------------------------------------------------------------------------------- /wrappers/picard/collectinsertsizemetrics/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule insert_size: 2 | input: 3 | "mapped/{sample}.bam" 4 | output: 5 | txt="stats/{sample}.isize.txt", 6 | pdf="stats/{sample}.isize.pdf" 7 | log: 8 | "logs/picard/insert_size/{sample}.log" 9 | params: 10 | # optional parameters (e.g. relax checks as below) 11 | "VALIDATION_STRINGENCY=LENIENT " 12 | "METRIC_ACCUMULATION_LEVEL=null " 13 | "METRIC_ACCUMULATION_LEVEL=SAMPLE" 14 | wrapper: 15 | "master/bio/picard/collectinsertsizemetrics" 16 | -------------------------------------------------------------------------------- /wrappers/samtools/stats/wrapper.py: -------------------------------------------------------------------------------- 1 | """Snakemake wrapper for trimming paired-end reads using cutadapt.""" 2 | 3 | __author__ = "Julian de Ruiter" 4 | __copyright__ = "Copyright 2017, Julian de Ruiter" 5 | __email__ = "julianderuiter@gmail.com" 6 | __license__ = "MIT" 7 | 8 | 9 | from snakemake.shell import shell 10 | 11 | 12 | extra = snakemake.params.get("extra", "") 13 | region = snakemake.params.get("region", "") 14 | log = snakemake.log_fmt_shell(stdout=False, stderr=True) 15 | 16 | 17 | shell("samtools stats {extra} {snakemake.input} {region} > {snakemake.output} {log}") 18 | -------------------------------------------------------------------------------- /wrappers/bcftools/reheader/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule bcftools_reheader: 2 | input: 3 | vcf="a.bcf", 4 | ## new header, can be omitted if "samples" is set 5 | header="header.txt", 6 | ## file containing new sample names, can be omitted if "header" is set 7 | samples="samples.tsv" 8 | output: 9 | "a.reheader.bcf" 10 | params: 11 | extra="", # optional parameters for bcftools reheader 12 | view_extra="-O b" # add output format for internal bcftools view call 13 | wrapper: 14 | "master/bio/bcftools/reheader" 15 | -------------------------------------------------------------------------------- /wrappers/gatk3/realignertargetcreator/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule realignertargetcreator: 2 | input: 3 | bam="mapped/{sample}.bam", 4 | ref="genome.fasta", 5 | known="dbsnp.vcf.gz", 6 | output: 7 | intervals="{sample}.intervals", 8 | java_temp=temp(directory("gatk3_indelrealigner/{sample}")), 9 | log: 10 | "logs/gatk/realignertargetcreator/{sample}.log", 11 | params: 12 | extra="", # optional 13 | resources: 14 | mem_mb=1024, 15 | threads: 16 16 | wrapper: 17 | "bio/gatk3/realignertargetcreator" 18 | -------------------------------------------------------------------------------- /wrappers/samtools/bam2fq/separate/meta.yaml: -------------------------------------------------------------------------------- 1 | name: samtools bam2fq separate 2 | description: 3 | Convert a bam file with paired end reads back to unaligned reads in a two 4 | separate fastq files with samtools. Reads that are not properly paired are 5 | discarded (READ_OTHER and singleton reads in samtools bam2fq documentation), 6 | as are secondary (0x100) and supplementary reads (0x800). 7 | authors: 8 | - David Laehnemann 9 | - Victoria Sack 10 | notes: | 11 | * Samtools -@/--threads takes one integer as input. This is the number of additional threads and not raw threads. 12 | -------------------------------------------------------------------------------- /dnaseq_slurm_hpf.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH --job-name=crg2 3 | #SBATCH --time=100:00:00 4 | #SBATCH --ntasks-per-node=1 5 | #SBATCH --mem=4G 6 | #SBATCH --output=%x-%j.out 7 | 8 | SF=~/crg2/Snakefile 9 | CP="/hpf/largeprojects/ccm_dccforge/dccdipg/Common/snakemake" 10 | SLURM=~/crg2/slurm_profile/ 11 | CONFIG=config_hpf.yaml 12 | 13 | module purge 14 | 15 | source /hpf/largeprojects/ccm_dccforge/dccdipg/Common/anaconda3/etc/profile.d/conda.sh 16 | conda activate snakemake 17 | 18 | snakemake --use-conda -s ${SF} --cores 4 --conda-prefix ${CP} --configfile ${CONFIG} --profile ${SLURM} 19 | -------------------------------------------------------------------------------- /wrappers/gatk/selectvariants/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Johannes Köster" 2 | __copyright__ = "Copyright 2018, Johannes Köster" 3 | __email__ = "johannes.koester@protonmail.com" 4 | __license__ = "MIT" 5 | 6 | 7 | from snakemake.shell import shell 8 | 9 | extra = snakemake.params.get("extra", "") 10 | java_opts = snakemake.params.get("java_opts", "") 11 | 12 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 13 | shell( 14 | "gatk --java-options '{java_opts}' SelectVariants -R {snakemake.input.ref} -V {snakemake.input.vcf} " 15 | "{extra} -O {snakemake.output.vcf} {log}" 16 | ) 17 | -------------------------------------------------------------------------------- /wrappers/picard/collectalignmentsummarymetrics/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule alignment_summary: 2 | input: 3 | ref="genome.fasta", 4 | bam="mapped/{sample}.bam" 5 | output: 6 | "stats/{sample}.summary.txt" 7 | log: 8 | "logs/picard/alignment-summary/{sample}.log" 9 | params: 10 | # optional parameters (e.g. relax checks as below) 11 | "VALIDATION_STRINGENCY=LENIENT " 12 | "METRIC_ACCUMULATION_LEVEL=null " 13 | "METRIC_ACCUMULATION_LEVEL=SAMPLE" 14 | wrapper: 15 | "master/bio/picard/collectalignmentsummarymetrics" 16 | -------------------------------------------------------------------------------- /wrappers/samtools/bam2fq/separate/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule samtools_bam2fq_separate: 2 | input: 3 | "mapped/{sample}.bam" 4 | output: 5 | "reads/{sample}.1.fq", 6 | "reads/{sample}.2.fq" 7 | params: 8 | sort = "-m 4G", 9 | bam2fq = "-n" 10 | threads: # Remember, this is the number of samtools' additional threads 11 | 3 # At least 2 threads have to be requested on cluster sumbission. 12 | # Thus, this value - 2 will be sent to samtools sort -@ argument. 13 | wrapper: 14 | "master/bio/samtools/bam2fq/separate" 15 | -------------------------------------------------------------------------------- /wrappers/bwa/aln/wrapper.py: -------------------------------------------------------------------------------- 1 | """Snakemake wrapper for bwa aln.""" 2 | 3 | __author__ = "Julian de Ruiter" 4 | __copyright__ = "Copyright 2017, Julian de Ruiter" 5 | __email__ = "julianderuiter@gmail.com" 6 | __license__ = "MIT" 7 | 8 | 9 | from snakemake.shell import shell 10 | 11 | 12 | extra = snakemake.params.get("extra", "") 13 | log = snakemake.log_fmt_shell(stdout=False, stderr=True) 14 | 15 | shell( 16 | "bwa aln" 17 | " {extra}" 18 | " -t {snakemake.threads}" 19 | " {snakemake.params.index}" 20 | " {snakemake.input[0]}" 21 | " > {snakemake.output[0]} {log}" 22 | ) 23 | -------------------------------------------------------------------------------- /wrappers/gatk/haplotypecaller/meta.yaml: -------------------------------------------------------------------------------- 1 | name: gatk HaplotypeCaller 2 | description: | 3 | Run gatk HaplotypeCaller. 4 | authors: 5 | - Johannes Köster 6 | - Jake VanCampen 7 | input: 8 | - bam file 9 | output: 10 | - GVCF file 11 | notes: | 12 | * The `java_opts` param allows for additional arguments to be passed to the java compiler, e.g. "-Xmx4G" for one, and "-Xmx4G -XX:ParallelGCThreads=10" for two options. 13 | * The `extra` param alllows for additional program arguments. 14 | * For more inforamtion see, https://software.broadinstitute.org/gatk/documentation/article?id=11050 15 | 16 | -------------------------------------------------------------------------------- /pbs_profile/config.yaml.save: -------------------------------------------------------------------------------- 1 | restart-times: 3 2 | cluster: "/home/amphan/crg2/pbs_profile/pbs-submit.py --depend \"{dependencies}\"" # 3 | cluster-status: "~/crg2/pbs_profile/pbs_status.py" # 4 | cluster-config: "~/crg2/pbs_profile/pbs-config.yaml" 5 | jobscript: "~/crg2/pbs_profile/pbs-jobscript.sh" 6 | max-jobs-per-second: 10 7 | max-status-checks-per-second: 10 8 | cores: 86 # how many jobs you want to submit to your cluster queue 9 | local-cores: 1 10 | rerun-incomplete: true # recomended for cluster submissions 11 | keep-going: false 12 | notemp: false 13 | immediate-submit: true 14 | verbose: true 15 | -------------------------------------------------------------------------------- /wrappers/gatk/genotypegvcfs/meta.yaml: -------------------------------------------------------------------------------- 1 | name: gatk GenotypeGVCFs 2 | description: | 3 | Run gatk GenotypeGVCFs. 4 | authors: 5 | - Johannes Köster 6 | - Jake VanCampen 7 | input: 8 | - GVCF files 9 | output: 10 | - VCF file with genotypes 11 | notes: | 12 | * The `java_opts` param allows for additional arguments to be passed to the java compiler, e.g. "-Xmx4G" for one, and "-Xmx4G -XX:ParallelGCThreads=10" for two options. 13 | * The `extra` param alllows for additional program arguments. 14 | * For more inforamtion see, https://software.broadinstitute.org/gatk/documentation/article?id=11050 15 | -------------------------------------------------------------------------------- /wrappers/gatk/splitncigarreads/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Jan Forster" 2 | __copyright__ = "Copyright 2019, Jan Forster" 3 | __email__ = "jan.forster@uk-essen.de" 4 | __license__ = "MIT" 5 | 6 | import os 7 | 8 | from snakemake.shell import shell 9 | 10 | extra = snakemake.params.get("extra", "") 11 | java_opts = snakemake.params.get("java_opts", "") 12 | 13 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 14 | shell( 15 | "gatk --java-options '{java_opts}' SplitNCigarReads {extra} " 16 | " -R {snakemake.input.ref} -I {snakemake.input.bam} " 17 | "-O {snakemake.output} {log}" 18 | ) 19 | -------------------------------------------------------------------------------- /wrappers/metasv/wrapper.py: -------------------------------------------------------------------------------- 1 | from snakemake.shell import shell 2 | 3 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 4 | 5 | 6 | shell( 7 | "(run_metasv.py " 8 | "--sample {snakemake.params.sample} " 9 | "--reference {snakemake.input.fasta} " 10 | "--bam {snakemake.input.bam} " 11 | "--outdir {snakemake.params.outdir} " 12 | "--lumpy_vcf {snakemake.input.lumpy} " 13 | "--manta_vcf {snakemake.input.manta} " 14 | "--wham_vcf {snakemake.input.wham} " 15 | "--num_threads {snakemake.threads} " 16 | "--disable_assembly " 17 | "--filter_gaps) {log}" 18 | ) 19 | -------------------------------------------------------------------------------- /wrappers/gatk/combinegvcfs/meta.yaml: -------------------------------------------------------------------------------- 1 | name: gatk CombineGVCFs 2 | description: | 3 | Run gatk CombineGVCFs. 4 | authors: 5 | - Johannes Köster 6 | - Jake VanCampen 7 | input: 8 | - GVCF files of multiple samples 9 | output: 10 | - Combined GVCF 11 | notes: | 12 | * The `java_opts` param allows for additional arguments to be passed to the java compiler, e.g. "-Xmx4G" for one, and "-Xmx4G -XX:ParallelGCThreads=10" for two options. 13 | * The `extra` param alllows for additional program arguments. 14 | * For more inforamtion see, https://software.broadinstitute.org/gatk/documentation/article?id=11050 15 | -------------------------------------------------------------------------------- /validation.pbs: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | #PBS -l walltime=72:00:00,nodes=1:ppn=1 4 | #PBS -joe . 5 | #PBS -d . 6 | #PBS -l vmem=80g,mem=80g 7 | #PBS -N validation 8 | 9 | 10 | #please change the following three variables according to your settings, as the recent crg2 repo is not copied over here 11 | 12 | CP="/hpf/largeprojects/ccm_dccforge/dccdipg/Common/snakemake"; 13 | PBS=~/crg2/pbs_profile; 14 | 15 | source /hpf/largeprojects/ccm_dccforge/dccdipg/Common/anaconda3/etc/profile.d/conda.sh 16 | conda activate snakemake 17 | 18 | snakemake --use-conda -s ~/crg2/validation.Snakefile --conda-prefix $CP --profile $PBS -pr 19 | -------------------------------------------------------------------------------- /wrappers/picard/mergesamfiles/wrapper.py: -------------------------------------------------------------------------------- 1 | """Snakemake wrapper for picard MergeSamFiles.""" 2 | 3 | __author__ = "Julian de Ruiter" 4 | __copyright__ = "Copyright 2017, Julian de Ruiter" 5 | __email__ = "julianderuiter@gmail.com" 6 | __license__ = "MIT" 7 | 8 | 9 | from snakemake.shell import shell 10 | 11 | 12 | inputs = " ".join("INPUT={}".format(in_) for in_ in snakemake.input) 13 | log = snakemake.log_fmt_shell(stdout=False, stderr=True) 14 | 15 | shell( 16 | "picard" 17 | " MergeSamFiles" 18 | " {snakemake.params}" 19 | " {inputs}" 20 | " OUTPUT={snakemake.output[0]}" 21 | " {log}" 22 | ) 23 | -------------------------------------------------------------------------------- /wrappers/vep/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule vcfanno: 2 | input: 3 | "{sample}.vcf", # (vcf, bcf, or vcf.gz) 4 | output: 5 | calls="vep/{sample}.vcf", # annotated calls (vcf, bcf, or vcf.gz) 6 | log: 7 | "logs/vep/{sample}.log" 8 | threads: 5 9 | resources: 10 | mem_mb = 30000 11 | params: 12 | dir: config["annotation"]["vep"]["dir"], 13 | maxentscan: config["annotation"]["vep"]["maxentscan"], 14 | human_ancestor_fasta: config["annotation"]["vep"]["human_ancestor_fasta"], 15 | ref: config["ref"]["genome"], 16 | wrapper: 17 | "master/bio/vep" 18 | -------------------------------------------------------------------------------- /utils/wgs_gene_coverage/README.md: -------------------------------------------------------------------------------- 1 | # Gene coverage scripts 2 | 3 | 1. ```get_gene_coverage.sh```: Generate cram coverage report from WES or WGS across exons/introns for given gene using mosdepth. 4 | 2. ```get_gene_exon_intron.py```: Generate BED with exon/intron coordiantes for query gene. Used in get_gene_coverage.sh. 5 | 3. ```parse_gtf.R```: Generate BED with exon/intron coordiantes for the hg19 genome from RefSeq GTF file. Output is used in get_gene_exon_intron.R to get coordinates for specific genes. 6 | 4. ```intron_region_coverage_for_WES.py```: Calculate coverage at 10,20,50,100,1000 bp into intron sequences (useful for WES) 7 | -------------------------------------------------------------------------------- /wrappers/samtools/merge/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Johannes Köster" 2 | __copyright__ = "Copyright 2016, Johannes Köster" 3 | __email__ = "koester@jimmy.harvard.edu" 4 | __license__ = "MIT" 5 | 6 | 7 | from snakemake.shell import shell 8 | 9 | # Samtools takes additional threads through its option -@ 10 | # One thread for samtools merge 11 | # Other threads are *additional* threads passed to the '-@' argument 12 | threads = "" if snakemake.threads <= 1 else " -@ {} ".format(snakemake.threads - 1) 13 | 14 | shell( 15 | "samtools merge {threads} {snakemake.params} " 16 | "{snakemake.output[0]} {snakemake.input}" 17 | ) 18 | -------------------------------------------------------------------------------- /wrappers/bwa/mem/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule bwa_mem: 2 | input: 3 | reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"] 4 | output: 5 | "mapped/{sample}.bam" 6 | log: 7 | "logs/bwa_mem/{sample}.log" 8 | params: 9 | index="genome", 10 | extra=r"-R '@RG\tID:{sample}\tSM:{sample}'", 11 | sort="none", # Can be 'none', 'samtools' or 'picard'. 12 | sort_order="queryname", # Can be 'queryname' or 'coordinate'. 13 | sort_extra="" # Extra args for samtools/picard. 14 | threads: 8 15 | wrapper: 16 | "master/bio/bwa/mem" 17 | -------------------------------------------------------------------------------- /wrappers/gatk/selectvariants/meta.yaml: -------------------------------------------------------------------------------- 1 | name: gatk SelectVariants 2 | description: | 3 | Run gatk SelectVariants. 4 | authors: 5 | - Johannes Köster 6 | - Jake VanCampen 7 | input: 8 | - vcf file 9 | - reference genome 10 | output: 11 | - filtered vcf file 12 | notes: | 13 | * The `java_opts` param allows for additional arguments to be passed to the java compiler, e.g. "-Xmx4G" for one, and "-Xmx4G -XX:ParallelGCThreads=10" for two options. 14 | * The `extra` param alllows for additional program arguments. 15 | * For more inforamtion see, https://software.broadinstitute.org/gatk/documentation/article?id=11050 16 | 17 | -------------------------------------------------------------------------------- /wrappers/bwa/mem/test/Snakefile_picard: -------------------------------------------------------------------------------- 1 | rule bwa_mem: 2 | input: 3 | reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"] 4 | output: 5 | "mapped/{sample}.bam" 6 | log: 7 | "logs/bwa_mem/{sample}.log" 8 | params: 9 | index="genome", 10 | extra=r"-R '@RG\tID:{sample}\tSM:{sample}'", 11 | sort="picard", # Can be 'none', 'samtools' or 'picard'. 12 | sort_order="queryname", # Can be 'queryname' or 'coordinate'. 13 | sort_extra="" # Extra args for samtools/picard. 14 | threads: 8 15 | wrapper: 16 | "master/bio/bwa/mem" 17 | -------------------------------------------------------------------------------- /wrappers/bwa/mem/test/Snakefile_samtools: -------------------------------------------------------------------------------- 1 | rule bwa_mem: 2 | input: 3 | reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"] 4 | output: 5 | "mapped/{sample}.bam" 6 | log: 7 | "logs/bwa_mem/{sample}.log" 8 | params: 9 | index="genome", 10 | extra=r"-R '@RG\tID:{sample}\tSM:{sample}'", 11 | sort="samtools", # Can be 'none', 'samtools' or 'picard'. 12 | sort_order="queryname", # Can be 'queryname' or 'coordinate'. 13 | sort_extra="" # Extra args for samtools/picard. 14 | threads: 8 15 | wrapper: 16 | "master/bio/bwa/mem" 17 | -------------------------------------------------------------------------------- /wrappers/gatk/variantfiltration/meta.yaml: -------------------------------------------------------------------------------- 1 | name: gatk VariantFiltration 2 | description: | 3 | Run gatk VariantFiltration. 4 | authors: 5 | - Johannes Köster 6 | - Jake VanCampen 7 | input: 8 | - vcf file 9 | - reference genome 10 | output: 11 | - filtered vcf file 12 | notes: | 13 | * The `java_opts` param allows for additional arguments to be passed to the java compiler, e.g. "-Xmx4G" for one, and "-Xmx4G -XX:ParallelGCThreads=10" for two options. 14 | * The `extra` param alllows for additional program arguments. 15 | * For more inforamtion see, https://software.broadinstitute.org/gatk/documentation/article?id=11050 16 | -------------------------------------------------------------------------------- /wrappers/gatk/variantrecalibrator/meta.yaml: -------------------------------------------------------------------------------- 1 | name: gatk VariantRecalibrator 2 | description: | 3 | Run gatk VariantRecalibrator. 4 | authors: 5 | - Johannes Köster 6 | - Jake VanCampen 7 | input: 8 | - VCF file 9 | output: 10 | - .recal file 11 | - .tranches file 12 | notes: | 13 | * The `java_opts` param allows for additional arguments to be passed to the java compiler, e.g. "-Xmx4G" for one, and "-Xmx4G -XX:ParallelGCThreads=10" for two options. 14 | * The `extra` param alllows for additional program arguments. 15 | * For more inforamtion see, https://software.broadinstitute.org/gatk/documentation/article?id=11050 16 | -------------------------------------------------------------------------------- /wrappers/picard/sortsam/wrapper.py: -------------------------------------------------------------------------------- 1 | """Snakemake wrapper for picard SortSam.""" 2 | 3 | __author__ = "Julian de Ruiter" 4 | __copyright__ = "Copyright 2017, Julian de Ruiter" 5 | __email__ = "julianderuiter@gmail.com" 6 | __license__ = "MIT" 7 | 8 | 9 | from snakemake.shell import shell 10 | 11 | 12 | extra = snakemake.params.get("extra", "") 13 | log = snakemake.log_fmt_shell(stdout=False, stderr=True) 14 | 15 | shell( 16 | "picard" 17 | " SortSam" 18 | " {extra}" 19 | " INPUT={snakemake.input[0]}" 20 | " OUTPUT={snakemake.output[0]}" 21 | " SORT_ORDER={snakemake.params.sort_order}" 22 | " {log}" 23 | ) 24 | -------------------------------------------------------------------------------- /wrappers/gatk/baserecalibrator/meta.yaml: -------------------------------------------------------------------------------- 1 | name: gatk BaseRecalibrator 2 | description: | 3 | Run gatk BaseRecalibrator and ApplyBQSR in one step. 4 | authors: 5 | - Johannes Köster 6 | - Jake VanCampen 7 | input: 8 | - bam file 9 | output: 10 | - recalibrated bam file 11 | notes: | 12 | * The `java_opts` param allows for additional arguments to be passed to the java compiler, e.g. "-Xmx4G" for one, and "-Xmx4G -XX:ParallelGCThreads=10" for two options. 13 | * The `extra` param alllows for additional program arguments. 14 | * For more inforamtion see, https://software.broadinstitute.org/gatk/documentation/article?id=11050 15 | 16 | -------------------------------------------------------------------------------- /wrappers/gatk/genotypegvcfs/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Johannes Köster" 2 | __copyright__ = "Copyright 2018, Johannes Köster" 3 | __email__ = "johannes.koester@protonmail.com" 4 | __license__ = "MIT" 5 | 6 | 7 | import os 8 | 9 | from snakemake.shell import shell 10 | 11 | 12 | extra = snakemake.params.get("extra", "") 13 | java_opts = snakemake.params.get("java_opts", "") 14 | 15 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 16 | shell( 17 | "gatk --java-options '{java_opts}' GenotypeGVCFs {extra} " 18 | "-V {snakemake.input.gvcf} " 19 | "-R {snakemake.input.ref} " 20 | "-O {snakemake.output.vcf} {log}" 21 | ) 22 | -------------------------------------------------------------------------------- /wrappers/manta/wrapper.py: -------------------------------------------------------------------------------- 1 | from snakemake.shell import shell 2 | 3 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 4 | 5 | shell( 6 | "(configManta.py " 7 | "--runDir {snakemake.params.outdir} " 8 | "--reference {snakemake.input.fasta} " 9 | "--bam {snakemake.input.bam} " 10 | "{snakemake.params.include_chroms}; " 11 | "cd {snakemake.params.outdir}; " 12 | "./runWorkflow.py " 13 | "--quiet " 14 | "-m local " 15 | "-j {snakemake.threads});" 16 | "(bcftools filter -i 'FORMAT/SR > 0 & BND_DEPTH >= 10 & MATE_BND_DEPTH >= 10' {snakemake.output.sv} -o {snakemake.output.bnd} -O z) {log}" 17 | ) 18 | -------------------------------------------------------------------------------- /wrappers/rtg-tools/vcfsubset/wrapper.py: -------------------------------------------------------------------------------- 1 | from snakemake.shell import shell 2 | 3 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 4 | 5 | java_opts = snakemake.params.get("java_opts") 6 | 7 | 8 | shell( 9 | "export _JAVA_OPTIONS=\"{java_opts}\" && " 10 | "rtg vcfsubset -i {snakemake.input} -o annotated/{snakemake.wildcards.p}/vcfanno/noDP.vcf.gz --remove-info DP && " 11 | "bcftools +fill-tags annotated/{snakemake.wildcards.p}/vcfanno/noDP.vcf.gz -o {snakemake.output} -- -t 'DP2=sum(DP)' && " 12 | "sed -i \"s/DP2/DP/g\" {snakemake.output} && " 13 | "rm annotated/{snakemake.wildcards.p}/vcfanno/noDP.vcf* " 14 | 15 | ) -------------------------------------------------------------------------------- /wrappers/snpeff/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule snpeff: 2 | input: 3 | "{sample}.vcf", # (vcf, bcf, or vcf.gz) 4 | output: 5 | calls="snpeff/{sample}.vcf", # annotated calls (vcf, bcf, or vcf.gz) 6 | stats="snpeff/{sample}.html", # summary statistics (in HTML), optional 7 | csvstats="snpeff/{sample}.csv" # summary statistics in CSV, optional 8 | log: 9 | "logs/snpeff/{sample}.log" 10 | params: 11 | reference="ebola_zaire", # reference name (from `snpeff databases`) 12 | extra="-Xmx4g" # optional parameters (e.g., max memory 4g) 13 | wrapper: 14 | "master/bio/snpeff" 15 | -------------------------------------------------------------------------------- /dnaseq_slurm_cheo_ri.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -A slurm 3 | #SBATCH --partition=all 4 | #SBATCH --job-name=crg2 5 | #SBATCH --time=100:00:00 6 | #SBATCH --ntasks-per-node=1 7 | #SBATCH --mem=4G 8 | #SBATCH --output=%x-%j.out 9 | 10 | SF="/srv/shared/pipelines/crg2/Snakefile" 11 | CP="/srv/shared/conda_envs/crg2-conda/" 12 | SLURM="/srv/shared/pipelines/crg2/slurm_profile/" 13 | CONFIG="config_cheo_ri.yaml" 14 | 15 | source /storage/modules/anaconda/2020.11/etc/profile.d/conda.sh 16 | conda activate /srv/shared/conda_envs/snakemake_5.10.0/ 17 | 18 | snakemake --use-conda -s ${SF} --cores 4 --conda-prefix ${CP} --configfile ${CONFIG} --profile ${SLURM} 19 | -------------------------------------------------------------------------------- /programs.03-18-2021.txt: -------------------------------------------------------------------------------- 1 | bcftools 1.10 2 | bcftools 1.9 3 | bedtools 2.29.0 4 | bowtie2 2.4.1 5 | bwa 0.7.17 6 | fastqc 0.11.8 7 | fastq-screen 0.13.0 8 | freebayes 1.3.1 9 | gatk4 4.1.4.1 10 | htslib 1.10 11 | manta 1.6.0 12 | metasv 0.5.4 13 | multiqc 1.7 14 | parallel 20190522 15 | picard 2.18.16 16 | picard 2.20.1 17 | picard 2.9.2 18 | pigz 2.3.4 19 | platypus-variant 0.8.1.2 20 | qualimap 21 | r-base 3.3.2 22 | sambamba 0.7.1 23 | samblaster 0.1.24 24 | samblaster 0.1.25 25 | samtools 1.10 26 | samtools 1.9 27 | sed 4.7 28 | smoove 0.2.5 29 | snpeff 4.3.1t 30 | vcftools 0.1.16 31 | verifybamid2==1.0.6 32 | vt 2015.11.10 33 | wham 1.8.0.1.2017.05.03 34 | -------------------------------------------------------------------------------- /scripts/str/str_helper.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | x=`samtools idxstats $1 | grep "X"`; 4 | y=`samtools idxstats $1 | grep "Y"`; 5 | xcov=`echo $x | awk '{ printf("%0.5f", $3/$2); }'`; 6 | ycov=`echo $y | awk '{ printf("%0.5f", $3/$2); }'`; 7 | 8 | # xcov=$(echo "scale=4; $(samtools idxstats $1 | grep "X" | cut -f 3)/$(samtools idxstats $1 | grep "X" | cut -f 2)" | bc) 9 | # ycov=$(echo "scale=4; $(samtools idxstats $1 | grep "Y" | cut -f 3)/$(samtools idxstats $1 | grep "Y" | cut -f 2)" | bc) 10 | rat=$(echo "scale=4; ${xcov}/${ycov}" | bc) 11 | if (( $(echo "$rat > 5.0" | bc -l) )); then 12 | sex=female 13 | else 14 | sex=male 15 | fi 16 | echo "$sex" -------------------------------------------------------------------------------- /wrappers/picard/collecttargetedpcrmetrics/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Patrik Smeds" 2 | __copyright__ = "Copyright 2019, Patrik Smeds" 3 | __email__ = "patrik.smeds@mail.com" 4 | __license__ = "MIT" 5 | 6 | 7 | from snakemake.shell import shell 8 | 9 | 10 | log = snakemake.log_fmt_shell() 11 | 12 | extra = snakemake.params.get("extra", "") 13 | 14 | shell( 15 | "picard CollectTargetedPcrMetrics " 16 | "{extra} " 17 | "INPUT={snakemake.input.bam} " 18 | "OUTPUT={snakemake.output[0]} " 19 | "AMPLICON_INTERVALS={snakemake.input.amplicon_intervals} " 20 | "TARGET_INTERVALS={snakemake.input.target_intervals} " 21 | "{log}" 22 | ) 23 | -------------------------------------------------------------------------------- /wrappers/picard/mergevcfs/wrapper.py: -------------------------------------------------------------------------------- 1 | """Snakemake wrapper for picard MergeSamFiles.""" 2 | 3 | __author__ = "Johannes Köster" 4 | __copyright__ = "Copyright 2018, Johannes Köster" 5 | __email__ = "johannes.koester@protonmail.com" 6 | __license__ = "MIT" 7 | 8 | 9 | from snakemake.shell import shell 10 | 11 | 12 | inputs = " ".join("INPUT={}".format(f) for f in snakemake.input.vcfs) 13 | log = snakemake.log_fmt_shell(stdout=False, stderr=True) 14 | extra = snakemake.params.get("extra", "") 15 | 16 | shell( 17 | "picard" 18 | " MergeVcfs" 19 | " {extra}" 20 | " {inputs}" 21 | " OUTPUT={snakemake.output[0]}" 22 | " {log}" 23 | ) 24 | -------------------------------------------------------------------------------- /wrappers/bcftools/annotate/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Aarthi Mohan" 2 | __copyright__ = "Copyright 2021, Aarthi Mohan" 3 | __email__ = "aarthi.mohan@sickkids.ca" 4 | __license__ = "MIT" 5 | 6 | 7 | from snakemake.shell import shell 8 | 9 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 10 | 11 | if not snakemake.threads: 12 | threads = 8 13 | else: 14 | threads = snakemake.threads 15 | 16 | shell( 17 | "bcftools annotate -a {snakemake.input.annot} -h {snakemake.input.hdr} " 18 | "-c CHROM,POS,REF,ALT,INFO/CALLERS,INFO/NUMCALLS " 19 | "--threads {threads} -o {snakemake.output} -O z " 20 | "{snakemake.input.vcf} {log}" 21 | ) 22 | -------------------------------------------------------------------------------- /wrappers/picard/gathervcfs/wrapper.py: -------------------------------------------------------------------------------- 1 | """Snakemake wrapper for picard MergeSamFiles.""" 2 | 3 | __author__ = "Johannes Köster" 4 | __copyright__ = "Copyright 2018, Johannes Köster" 5 | __email__ = "johannes.koester@protonmail.com" 6 | __license__ = "MIT" 7 | 8 | 9 | from snakemake.shell import shell 10 | 11 | 12 | inputs = " ".join("INPUT={}".format(f) for f in snakemake.input.vcfs) 13 | log = snakemake.log_fmt_shell(stdout=False, stderr=True) 14 | extra = snakemake.params.get("extra", "") 15 | 16 | shell( 17 | "picard" 18 | " GatherVcfs" 19 | " {extra}" 20 | " {inputs}" 21 | " OUTPUT={snakemake.output.gvcf}" 22 | " {log}" 23 | ) 24 | -------------------------------------------------------------------------------- /utils/check_dup_rate.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | family=$1 3 | multiqc=`echo $family/qc/multiqc/multiqc_data/multiqc_picard_dups.txt` 4 | dups=(`cat $multiqc | awk -F '\t' '{print $10}'`) 5 | samples=(`cat $multiqc | awk -F '\t' '{print $1}'`) 6 | num_of_samples=$((`echo ${#samples[@]}`-1)) 7 | 8 | for i in `seq 1 $num_of_samples` 9 | do 10 | dup_rate=`awk "BEGIN {print ${dups[i]}*100}" | cut -d '.' -f1` 11 | sample=`echo ${samples[i]}` 12 | if (( $dup_rate >= "20")); then 13 | echo "$sample in $family has greater than 20% duplication rate, run coverage metrics: ${dups[i]}" 14 | else 15 | echo "$sample in $family duplication rate OK: ${dups[i]}" 16 | fi 17 | done 18 | 19 | -------------------------------------------------------------------------------- /wrappers/bcftools/stats/wrapper.py: -------------------------------------------------------------------------------- 1 | from snakemake.shell import shell 2 | import os.path 3 | from os import path 4 | 5 | 6 | 7 | extra = snakemake.params.get("extra", "") 8 | vcf = snakemake.input[0] 9 | 10 | 11 | shell( 12 | "bcftools stats -s - {vcf} > {snakemake.output[0]}" 13 | ) 14 | 15 | #rename sample name in output file 16 | dir = os.path.dirname(snakemake.output[0]) 17 | base = path.basename(snakemake.output[0]).split('.')[0] 18 | new_base = base + "_stats.txt" 19 | new_path = path.join(dir, new_base) 20 | 21 | shell( 22 | " sed s/-gatk4//g {snakemake.output[0]} > {new_path} && rm {snakemake.output[0]} " 23 | "&& mv {new_path} {snakemake.output[0]} ") 24 | -------------------------------------------------------------------------------- /wrappers/gatk/combinegvcfs/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Johannes Köster" 2 | __copyright__ = "Copyright 2018, Johannes Köster" 3 | __email__ = "johannes.koester@protonmail.com" 4 | __license__ = "MIT" 5 | 6 | 7 | import os 8 | 9 | from snakemake.shell import shell 10 | 11 | 12 | extra = snakemake.params.get("extra", "") 13 | java_opts = snakemake.params.get("java_opts", "") 14 | gvcfs = list(map("-V {}".format, snakemake.input.gvcfs)) 15 | 16 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 17 | shell( 18 | "gatk --java-options '{java_opts}' CombineGVCFs {extra} " 19 | "{gvcfs} " 20 | "-R {snakemake.input.ref} " 21 | "-O {snakemake.output.gvcf} {log}" 22 | ) 23 | -------------------------------------------------------------------------------- /dnaseq_cluster.pbs: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | #PBS -l walltime=72:00:00,nodes=1:ppn=1 4 | #PBS -joe . 5 | #PBS -d . 6 | #PBS -l vmem=30g,mem=30g 7 | #PBS -N crg2_pbs 8 | 9 | 10 | #please change the following three variables according to your settings, as the recent crg2 repo is not copied over here 11 | 12 | 13 | SF=~/crg2/Snakefile; 14 | CP="/hpf/largeprojects/ccm_dccforge/dccdipg/Common/snakemake"; 15 | PBS=~/crg2/pbs_profile; 16 | CONFIG=config_hpf.yaml 17 | 18 | source /hpf/largeprojects/ccm_dccforge/dccdipg/Common/anaconda3/etc/profile.d/conda.sh 19 | conda activate snakemake 20 | 21 | snakemake --use-conda -s ${SF} --conda-prefix ${CP} --profile ${PBS} --configfile ${CONFIG} -p 22 | -------------------------------------------------------------------------------- /pbs_profile/config.yaml: -------------------------------------------------------------------------------- 1 | cluster: "pbs_submit.py" 2 | 3 | #pbs_submit.py --depend \"{dependencies}\" -> use this only when you 4 | #set immediate-submit:true. 5 | 6 | cluster-status: "pbs_status.py" # 7 | cluster-config: "pbs_config.yaml" #copy this from crg2/pbs_profile/ to the directory running snakemake 8 | jobscript: "pbs_jobscript.sh" 9 | max-jobs-per-second: 10 10 | max-status-checks-per-second: 1 11 | cores: 100 # how many jobs you want to submit to your cluster queue 12 | local-cores: 1 13 | rerun-incomplete: true # recommended for cluster submissions 14 | restart-times: 3 15 | keep-going: false 16 | notemp: false 17 | immediate-submit: false 18 | latency-wait: 60 19 | verbose: true 20 | -------------------------------------------------------------------------------- /rules/validation.smk: -------------------------------------------------------------------------------- 1 | rule benchmark: 2 | input: 3 | vcf="annotated/coding/vcfanno/{family}.coding.vep.vcfanno.vcf.gz", 4 | tbi="annotated/coding/vcfanno/{family}.coding.vep.vcfanno.vcf.gz.tbi", 5 | benchmark = config["validation"]["benchmark"] 6 | output: 7 | directory("validation/{family}"), 8 | log: 9 | "logs/benchmark/{family}-vcfeval.log" 10 | params: 11 | java_opts=config["params"]["rtg-tools"]["java_opts"], 12 | pipeline=config["run"]["pipeline"], 13 | sdf = config["params"]["rtg-tools"]["vcfeval"]["sdf"] 14 | resources: 15 | mem=30 16 | wrapper: 17 | get_wrapper_path("rtg-tools", "vcfeval") 18 | -------------------------------------------------------------------------------- /wrappers/bcftools/isec/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Aarthi Mohan" 2 | __copyright__ = "Copyright 2021, Aarthi Mohan" 3 | __email__ = "aarthi.mohan@sickkids.ca" 4 | __license__ = "MIT" 5 | 6 | 7 | from snakemake.shell import shell 8 | 9 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 10 | 11 | if not snakemake.threads: 12 | threads = 8 13 | else: 14 | threads = snakemake.threads 15 | 16 | filters = snakemake.params.get("filters", "") 17 | if filters: 18 | filters = " -f '{}' ".format(filters) 19 | 20 | shell( 21 | "bcftools isec -n {snakemake.params.numpass} {filters} -O z --threads {threads} -p {snakemake.params.outdir} " 22 | "{snakemake.input.vcf} {log}" 23 | 24 | ) 25 | -------------------------------------------------------------------------------- /wrappers/mity/normalise/wrapper.py: -------------------------------------------------------------------------------- 1 | from snakemake.shell import shell 2 | 3 | log = snakemake.log_fmt_shell(stdout=True, stderr=True,append=True) 4 | 5 | family = snakemake.wildcards.family 6 | outdir = snakemake.params.outdir 7 | tool = snakemake.params.tool 8 | pythonpath = tool.replace("bin", "") 9 | 10 | python = " export PYTHONPATH={pythonpath}; " 11 | mity = " {tool}/mity normalise --prefix {family}.mity --output-dir {outdir} {snakemake.input};" 12 | vt = " vt decompose_blocksub -o {outdir}/{family}.mity.normalise.decompose.vcf.gz {outdir}/{family}.mity.normalise.vcf.gz;" 13 | tabix = " tabix {outdir}/{family}.mity.normalise.decompose.vcf.gz " 14 | shell("(" + python + mity + vt + tabix + ") {log}") -------------------------------------------------------------------------------- /wrappers/samblaster/wrapper.py: -------------------------------------------------------------------------------- 1 | from snakemake.shell import shell 2 | 3 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 4 | 5 | splitters = snakemake.output.splitters.replace('bam', 'sam') 6 | discordants = snakemake.output.discordants.replace('bam', 'sam') 7 | shell( 8 | "samtools view -h {snakemake.input} " 9 | "| samblaster " 10 | "--acceptDupMarks " 11 | "--excludeDups " 12 | "--addMateTags -M " 13 | "--splitterFile splitters " 14 | "--discordantFile discordants " 15 | "--ignoreUnmated " 16 | "-o /dev/null; " 17 | "samtools view -Sb splitters > {snakemake.output.splitters}; " 18 | "samtools view -Sb discordants > {snakemake.output.discordants}" 19 | ) 20 | -------------------------------------------------------------------------------- /wrappers/samtools/sort/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Johannes Köster" 2 | __copyright__ = "Copyright 2016, Johannes Köster" 3 | __email__ = "koester@jimmy.harvard.edu" 4 | __license__ = "MIT" 5 | 6 | 7 | import os 8 | from snakemake.shell import shell 9 | 10 | 11 | prefix = os.path.splitext(snakemake.output[0])[0] 12 | 13 | # Samtools takes additional threads through its option -@ 14 | # One thread for samtools 15 | # Other threads are *additional* threads passed to the argument -@ 16 | threads = "" if snakemake.threads <= 1 else " -@ {} ".format(snakemake.threads - 1) 17 | 18 | shell( 19 | "samtools sort {snakemake.params} {threads} -o {snakemake.output[0]} " 20 | "-T {prefix} {snakemake.input[0]}" 21 | ) 22 | -------------------------------------------------------------------------------- /wrappers/gatk3/printreads/meta.yaml: -------------------------------------------------------------------------------- 1 | name: gatk3 PrintReads 2 | description: | 3 | Run gatk3 PrintReads 4 | authors: 5 | - Patrik Smeds 6 | input: 7 | - bam file 8 | - recalibration table 9 | - reference genome 10 | output: 11 | - bam file 12 | notes: | 13 | * The `java_opts` param allows for additional arguments to be passed to the java compiler, e.g. "-Xmx4G" for one, and "-Xmx4G -XX:ParallelGCThreads=10" for two options. 14 | * The `extra` param alllows for additional program arguments. 15 | * For more inforamtion see, https://software.broadinstitute.org/gatk/documentation/article?id=11050 16 | * Gatk3.jar is not included in the bioconda package, i.e it need to be added to the conda environment manually. 17 | -------------------------------------------------------------------------------- /wrappers/gatk3/indelrealigner/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule indelrealigner: 2 | input: 3 | bam="mapped/{sample}.bam", 4 | bai="mapped/{sample}.bai", 5 | ref="genome.fasta", 6 | known="dbsnp.vcf.gz", 7 | known_idx="dbsnp.vcf.gz.tbi", 8 | target_intervals="{sample}.intervals" 9 | output: 10 | bam="realigned/{sample}.bam", 11 | bai="realigned/{sample}.bai", 12 | java_temp=temp(directory("/tmp/gatk3_indelrealigner/{sample}")), 13 | log: 14 | "logs/gatk3/indelrealigner/{sample}.log" 15 | params: 16 | extra="" # optional 17 | threads: 16 18 | resources: 19 | mem_mb = 1024 20 | wrapper: 21 | "bio/gatk/indelrealigner" 22 | -------------------------------------------------------------------------------- /wrappers/gatk3/printreads/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Patrik Smeds" 2 | __copyright__ = "Copyright 2019, Patrik Smeds" 3 | __email__ = "patrik.smeds@gmail.com.com" 4 | __license__ = "MIT" 5 | 6 | import os 7 | 8 | from snakemake.shell import shell 9 | 10 | extra = snakemake.params.get("extra", "") 11 | 12 | input_bam = snakemake.input.bam 13 | input_recal_data = snakemake.input.recal_data 14 | input_ref = snakemake.input.ref 15 | 16 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 17 | 18 | shell( 19 | "gatk3 {snakemake.params.java_opts} -T PrintReads" 20 | " {extra}" 21 | " -I {input_bam}" 22 | " -R {input_ref}" 23 | " -BQSR {input_recal_data}" 24 | " -o {snakemake.output}" 25 | " {log}" 26 | ) 27 | -------------------------------------------------------------------------------- /wrappers/smoove/wrapper.py: -------------------------------------------------------------------------------- 1 | from snakemake.shell import shell 2 | 3 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 4 | 5 | if snakemake.params.exclude_chroms: 6 | excludechroms = "--excludechroms {}".format(snakemake.params.exclude_chroms) 7 | else: 8 | excludechroms = "" 9 | shell( 10 | "(export TMPDIR={snakemake.params.outdir}; echo $TMPDIR; " 11 | "smoove call -x " 12 | "--name {snakemake.params.name} " 13 | "--outdir {snakemake.params.outdir} " 14 | "--fasta {snakemake.input.fasta} " 15 | "-p {snakemake.threads} " 16 | "--genotype " 17 | "{excludechroms} " 18 | "{snakemake.input.bam}) {log}; " 19 | "cd {snakemake.params.outdir}; " 20 | "rm *.bam* *.histo ;" 21 | ) 22 | -------------------------------------------------------------------------------- /wrappers/gatk3/baserecalibrator/meta.yaml: -------------------------------------------------------------------------------- 1 | name: gatk3 BaseRecalibrator 2 | description: | 3 | Run gatk3 BaseRecalibrator. 4 | authors: 5 | - Patrik Smeds 6 | input: 7 | - bam file 8 | - vcf files 9 | - reference genome 10 | output: 11 | - recalibration table 12 | notes: | 13 | * The `java_opts` param allows for additional arguments to be passed to the java compiler, e.g. "-Xmx4G" for one, and "-Xmx4G -XX:ParallelGCThreads=10" for two options. 14 | * The `extra` param alllows for additional program arguments. 15 | * For more inforamtion see, https://software.broadinstitute.org/gatk/documentation/article?id=11050 16 | * Gatk3.jar is not included in the bioconda package, i.e it need to be added to the conda environment manually. 17 | -------------------------------------------------------------------------------- /wrappers/igv-reports/wrapper.py: -------------------------------------------------------------------------------- 1 | """Snakemake wrapper for igv-reports.""" 2 | 3 | __author__ = "Johannes Köster" 4 | __copyright__ = "Copyright 2019, Johannes Köster" 5 | __email__ = "johannes.koester@uni-due.de" 6 | __license__ = "MIT" 7 | 8 | from snakemake.shell import shell 9 | 10 | extra = snakemake.params.get("extra", "") 11 | 12 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 13 | 14 | tracks = snakemake.input.get("tracks", []) 15 | if tracks: 16 | if isinstance(tracks, str): 17 | tracks = [tracks] 18 | tracks = "--tracks {}".format(" ".join(tracks)) 19 | 20 | shell( 21 | "create_report {extra} --standalone --output {snakemake.output[0]} {snakemake.input.vcf} {snakemake.input.fasta} {tracks} {log}" 22 | ) 23 | -------------------------------------------------------------------------------- /wrappers/vcftools/filter/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Patrik Smeds" 2 | __copyright__ = "Copyright 2018, Patrik Smeds" 3 | __email__ = "patrik.smeds@gmail.com" 4 | __license__ = "MIT" 5 | 6 | 7 | from snakemake.shell import shell 8 | 9 | input_flag = "--vcf" 10 | if snakemake.input[0].endswith(".gz"): 11 | input_flag = "--gzvcf" 12 | 13 | output = " > " + snakemake.output[0] 14 | if output.endswith(".gz"): 15 | output = " | gzip" + output 16 | 17 | log = snakemake.log_fmt_shell(stdout=False, stderr=True) 18 | 19 | extra = snakemake.params.get("extra", "") 20 | 21 | shell( 22 | "vcftools " 23 | "{input_flag} " 24 | "{snakemake.input} " 25 | "{extra} " 26 | "--recode " 27 | "--stdout " 28 | "{output} " 29 | "{log}" 30 | ) 31 | -------------------------------------------------------------------------------- /wrappers/bcftools/reheader/test/header.txt: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.0 2 | ##FILTER= 3 | ##FILTER= 4 | ##FILTER= 5 | ##INFO= 6 | ##INFO= 7 | ##FORMAT= 8 | ##FORMAT= 9 | ##FORMAT= 10 | ##contig= 11 | ##contig= 12 | ##contig= 13 | ##ALT= 14 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A 15 | -------------------------------------------------------------------------------- /wrappers/bwa/samse/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule bwa_samse: 2 | input: 3 | fastq="reads/{sample}.1.fastq", 4 | sai="sai/{sample}.1.sai" 5 | output: 6 | "mapped/{sample}.bam" 7 | params: 8 | index="genome", 9 | extra=r"-r '@RG\tID:{sample}\tSM:{sample}'", # optional: Extra parameters for bwa. 10 | sort="none", # optional: Enable sorting. Possible values: 'none', 'samtools' or 'picard'` 11 | sort_order="queryname", # optional: Sort by 'queryname' or 'coordinate' 12 | sort_extra="" # optional: extra arguments for samtools/picard 13 | log: 14 | "logs/bwa_samse/{sample}.log" 15 | wrapper: 16 | "master/bio/bwa/samse" 17 | -------------------------------------------------------------------------------- /wrappers/gatk/variantfiltration/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Johannes Köster" 2 | __copyright__ = "Copyright 2018, Johannes Köster" 3 | __email__ = "johannes.koester@protonmail.com" 4 | __license__ = "MIT" 5 | 6 | 7 | from snakemake.shell import shell 8 | 9 | extra = snakemake.params.get("extra", "") 10 | java_opts = snakemake.params.get("java_opts", "") 11 | filters = [ 12 | "--filter-name {} --filter-expression '{}'".format(name, expr.replace("'", "\\'")) 13 | for name, expr in snakemake.params.filters.items() 14 | ] 15 | 16 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 17 | shell( 18 | "gatk --java-options '{java_opts}' VariantFiltration -R {snakemake.input.ref} -V {snakemake.input.vcf} " 19 | "{extra} {filters} -O {snakemake.output.vcf} {log}" 20 | ) 21 | -------------------------------------------------------------------------------- /wrappers/multiqc/wrapper.py: -------------------------------------------------------------------------------- 1 | """Snakemake wrapper for trimming paired-end reads using cutadapt.""" 2 | 3 | __author__ = "Julian de Ruiter" 4 | __copyright__ = "Copyright 2017, Julian de Ruiter" 5 | __email__ = "julianderuiter@gmail.com" 6 | __license__ = "MIT" 7 | 8 | 9 | from os import path 10 | 11 | from snakemake.shell import shell 12 | 13 | 14 | input_dirs = set(path.dirname(fp) for fp in snakemake.input) 15 | output_dir = path.dirname(snakemake.output.report) 16 | output_name = path.basename(snakemake.output.report) 17 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 18 | 19 | shell( 20 | "multiqc" 21 | " -c {snakemake.params}" 22 | " --force" 23 | " -o {output_dir}" 24 | " -n {output_name}" 25 | " {input_dirs}" 26 | " {log}" 27 | ) 28 | -------------------------------------------------------------------------------- /wrappers/picard/collecthsmetrics/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule picard_collect_hs_metrics: 2 | input: 3 | bam="mapped/{sample}.bam", 4 | reference="genome.fasta", 5 | # Baits and targets should be given as interval lists. These can 6 | # be generated from bed files using picard BedToIntervalList. 7 | bait_intervals="regions.intervals", 8 | target_intervals="regions.intervals" 9 | output: 10 | "stats/hs_metrics/{sample}.txt" 11 | params: 12 | # Optional extra arguments. Here we reduce sample size 13 | # to reduce the runtime in our unit test. 14 | "SAMPLE_SIZE=1000" 15 | log: 16 | "logs/picard_collect_hs_metrics/{sample}.log" 17 | wrapper: 18 | "master/bio/picard/collecthsmetrics" 19 | -------------------------------------------------------------------------------- /wrappers/vt/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Dennis Kao" 2 | __copyright__ = "Copyright 2020, Dennis Kao" 3 | __email__ = "dennis.kao@sickkids.ca" 4 | __license__ = "BSD" 5 | 6 | 7 | from snakemake.shell import shell 8 | from os import path 9 | import shutil 10 | import tempfile 11 | 12 | shell.executable("bash") 13 | 14 | fasta = snakemake.params.get("ref") 15 | if fasta: 16 | fastaprefix = "-r {}".format(fasta) 17 | else: 18 | raise Exception("Missing reference fasta file.") 19 | 20 | outcalls = snakemake.output[0] 21 | 22 | incalls = snakemake.input[0] 23 | 24 | log = snakemake.log_fmt_shell(stdout=False, stderr=True) 25 | 26 | shell( 27 | "(vt decompose -s {incalls} | vt normalize {fastaprefix} -n - | vt uniq - " 28 | " | vt view -o {outcalls} - ) {log}" 29 | ) 30 | -------------------------------------------------------------------------------- /wrappers/bwa/samse/test/Snakefile_picard: -------------------------------------------------------------------------------- 1 | rule bwa_samse: 2 | input: 3 | fastq="reads/{sample}.1.fastq", 4 | sai="sai/{sample}.1.sai" 5 | output: 6 | "mapped/{sample}.bam" 7 | params: 8 | index="genome", 9 | extra=r"-r '@RG\tID:{sample}\tSM:{sample}'", # optional: Extra parameters for bwa. 10 | sort="picard", # optional: Enable sorting. Possible values: 'none', 'samtools' or 'picard'` 11 | sort_order="queryname", # optional: Sort by 'queryname' or 'coordinate' 12 | sort_extra="" # optional: extra arguments for samtools/picard 13 | log: 14 | "logs/bwa_samse/{sample}.log" 15 | wrapper: 16 | "master/bio/bwa/samse" 17 | -------------------------------------------------------------------------------- /wrappers/gatk/mutect/wrapper.py: -------------------------------------------------------------------------------- 1 | """Snakemake wrapper for GATK4 Mutect2""" 2 | 3 | __author__ = "Thibault Dayris" 4 | __copyright__ = "Copyright 2019, Dayris Thibault" 5 | __email__ = "thibault.dayris@gustaveroussy.fr" 6 | __license__ = "MIT" 7 | 8 | from snakemake.shell import shell 9 | from snakemake.utils import makedirs 10 | 11 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 12 | 13 | shell( 14 | "gatk Mutect2 " # Tool and its subprocess 15 | "--input {snakemake.input.map} " # Path to input mapping file 16 | "--output {snakemake.output.vcf} " # Path to output vcf file 17 | "--reference {snakemake.input.fasta} " # Path to reference fasta file 18 | "--germline-resource {snakemake.input.gnomad_germline} " 19 | "{log}" # Logging behaviour 20 | ) 21 | -------------------------------------------------------------------------------- /wrappers/bwa/samse/test/Snakefile_samtools: -------------------------------------------------------------------------------- 1 | rule bwa_samse: 2 | input: 3 | fastq="reads/{sample}.1.fastq", 4 | sai="sai/{sample}.1.sai" 5 | output: 6 | "mapped/{sample}.bam" 7 | params: 8 | index="genome", 9 | extra=r"-r '@RG\tID:{sample}\tSM:{sample}'", # optional: Extra parameters for bwa. 10 | sort="samtools", # optional: Enable sorting. Possible values: 'none', 'samtools' or 'picard'` 11 | sort_order="queryname", # optional: Sort by 'queryname' or 'coordinate' 12 | sort_extra="" # optional: extra arguments for samtools/picard 13 | log: 14 | "logs/bwa_samse/{sample}.log" 15 | wrapper: 16 | "master/bio/bwa/samse" 17 | -------------------------------------------------------------------------------- /rules/stats.smk: -------------------------------------------------------------------------------- 1 | rule vcf_to_tsv: 2 | input: 3 | "annotated/coding/vcfanno/{family}.coding.vep.vcfanno.vcf".format(family=project) 4 | output: 5 | report("tables/calls.tsv.gz", caption="../report/calls.rst", category="Calls") 6 | conda: 7 | "../envs/rbt.yaml" 8 | shell: 9 | "rbt vcf-to-txt -g --fmt DP AD --info ANN < {input} | " 10 | "gzip > {output}" 11 | 12 | 13 | rule plot_stats: 14 | input: 15 | "tables/calls.tsv.gz" 16 | output: 17 | depths=report("plots/depths.svg", caption="../report/depths.rst", category="Plots"), 18 | freqs=report("plots/allele-freqs.svg", caption="../report/freqs.rst", category="Plots") 19 | conda: 20 | "../envs/stats.yaml" 21 | script: 22 | "../scripts/plot-depths.py" 23 | -------------------------------------------------------------------------------- /wrappers/bedtools/coveragebed/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Patrik Smeds" 2 | __copyright__ = "Copyright 2019, Patrik Smeds" 3 | __email__ = "patrik.smeds@gmail.com" 4 | __license__ = "MIT" 5 | 6 | 7 | from snakemake.shell import shell 8 | 9 | shell.executable("bash") 10 | 11 | log = snakemake.log_fmt_shell(stdout=False, stderr=True) 12 | 13 | extra_params = snakemake.params.get("extra", "") 14 | 15 | input_a = snakemake.input.a 16 | input_b = snakemake.input.b 17 | 18 | output_file = snakemake.output[0] 19 | 20 | if not isinstance(output_file, str) and len(snakemake.output) != 1: 21 | raise ValueError("Output should be one file: " + str(output_file) + "!") 22 | 23 | shell( 24 | "coverageBed" 25 | " -a {input_a}" 26 | " -b {input_b}" 27 | " {extra_params}" 28 | " > {output_file}" 29 | " {log}" 30 | ) 31 | -------------------------------------------------------------------------------- /wrappers/bwa/sampe/test/Snakefile: -------------------------------------------------------------------------------- 1 | rule bwa_sampe: 2 | input: 3 | fastq=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"], 4 | sai=["sai/{sample}.1.sai", "sai/{sample}.2.sai"] 5 | output: 6 | "mapped/{sample}.bam" 7 | params: 8 | index="genome", 9 | extra=r"-r '@RG\tID:{sample}\tSM:{sample}'", # optional: Extra parameters for bwa. 10 | sort="none", # optional: Enable sorting. Possible values: 'none', 'samtools' or 'picard'` 11 | sort_order="queryname", # optional: Sort by 'queryname' or 'coordinate' 12 | sort_extra="" # optional: extra arguments for samtools/picard 13 | log: 14 | "logs/bwa_sampe/{sample}.log" 15 | wrapper: 16 | "master/bio/bwa/sampe" 17 | -------------------------------------------------------------------------------- /wrappers/bcftools/merge/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Patrik Smeds" 2 | __copyright__ = "Copyright 2018, Patrik Smeds" 3 | __email__ = "patrik.smeds@gmail.com" 4 | __license__ = "MIT" 5 | 6 | 7 | from snakemake.shell import shell 8 | 9 | extra = snakemake.params.get("extra", "") 10 | 11 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 12 | 13 | input = " ".join(snakemake.input.vcf) 14 | 15 | # if one sample, pass this rule, else merge into multisample vcf 16 | if len(snakemake.input.vcf) == 1: 17 | shell( 18 | "mv {snakemake.input.vcf} {snakemake.output.vcf_unsort} " 19 | ) 20 | 21 | else: 22 | shell( 23 | "bcftools merge {extra} -o {snakemake.output.vcf_unsort} " 24 | "{input} " 25 | ) 26 | 27 | 28 | shell( 29 | "bcftools sort {snakemake.output.vcf_unsort} " 30 | "-o {snakemake.output.vcf} " 31 | ) 32 | -------------------------------------------------------------------------------- /wrappers/bwa/sampe/test/Snakefile_picard: -------------------------------------------------------------------------------- 1 | rule bwa_sampe: 2 | input: 3 | fastq=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"], 4 | sai=["sai/{sample}.1.sai", "sai/{sample}.2.sai"] 5 | output: 6 | "mapped/{sample}.bam" 7 | params: 8 | index="genome", 9 | extra=r"-r '@RG\tID:{sample}\tSM:{sample}'", # optional: Extra parameters for bwa. 10 | sort="picard", # optional: Enable sorting. Possible values: 'none', 'samtools' or 'picard'` 11 | sort_order="queryname", # optional: Sort by 'queryname' or 'coordinate' 12 | sort_extra="" # optional: extra arguments for samtools/picard 13 | log: 14 | "logs/bwa_sampe/{sample}.log" 15 | wrapper: 16 | "master/bio/bwa/sampe" 17 | -------------------------------------------------------------------------------- /wrappers/bwa/sampe/test/Snakefile_samtools: -------------------------------------------------------------------------------- 1 | rule bwa_sampe: 2 | input: 3 | fastq=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"], 4 | sai=["sai/{sample}.1.sai", "sai/{sample}.2.sai"] 5 | output: 6 | "mapped/{sample}.bam" 7 | params: 8 | index="genome", 9 | extra=r"-r '@RG\tID:{sample}\tSM:{sample}'", # optional: Extra parameters for bwa. 10 | sort="samtools", # optional: Enable sorting. Possible values: 'none', 'samtools' or 'picard'` 11 | sort_order="queryname", # optional: Sort by 'queryname' or 'coordinate' 12 | sort_extra="" # optional: extra arguments for samtools/picard 13 | log: 14 | "logs/bwa_sampe/{sample}.log" 15 | wrapper: 16 | "master/bio/bwa/sampe" 17 | -------------------------------------------------------------------------------- /wrappers/snpeff/wrapper.py: -------------------------------------------------------------------------------- 1 | from snakemake.shell import shell 2 | 3 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 4 | 5 | # replace symbolic alleles so that snpeff will annotate against genes 6 | # https://github.com/pcingola/SnpEff/issues/344 7 | replace_ins = "zcat {snakemake.input} | sed 's//N/g' | sed 's//N/g' | sed 's//N/g' | sed 's//N/g' > tmp.vcf; " 8 | gzip_vcf = "bgzip --force tmp.vcf; " 9 | mv_vcf = "mv tmp.vcf.gz {snakemake.input}; " 10 | 11 | shell( 12 | "(" + replace_ins + gzip_vcf + mv_vcf + "snpEff {snakemake.params.java_opts} " 13 | "-i VCF " 14 | "-o VCF " 15 | "-dataDir {snakemake.params.data_dir} " 16 | "-s {snakemake.output.report} " 17 | "{snakemake.params.reference} " 18 | "{snakemake.input} > {snakemake.output.vcf}) {log}" 19 | ) 20 | -------------------------------------------------------------------------------- /wrappers/picard/collecthsmetrics/wrapper.py: -------------------------------------------------------------------------------- 1 | """Snakemake wrapper for picard CollectHSMetrics.""" 2 | 3 | __author__ = "Julian de Ruiter" 4 | __copyright__ = "Copyright 2017, Julian de Ruiter" 5 | __email__ = "julianderuiter@gmail.com" 6 | __license__ = "MIT" 7 | 8 | 9 | from snakemake.shell import shell 10 | 11 | 12 | inputs = " ".join("INPUT={}".format(in_) for in_ in snakemake.input) 13 | extra = snakemake.params.get("extra", "") 14 | log = snakemake.log_fmt_shell(stdout=False, stderr=True) 15 | 16 | shell( 17 | "picard CollectHsMetrics" 18 | " {extra}" 19 | " INPUT={snakemake.input.bam}" 20 | " OUTPUT={snakemake.output[0]}" 21 | " REFERENCE_SEQUENCE={snakemake.input.reference}" 22 | " BAIT_INTERVALS={snakemake.input.bait_intervals}" 23 | " TARGET_INTERVALS={snakemake.input.target_intervals}" 24 | " {log}" 25 | ) 26 | -------------------------------------------------------------------------------- /wrappers/samtools/fixmate/wrapper.py: -------------------------------------------------------------------------------- 1 | """Snakemake wrapper for samtools fixmate""" 2 | 3 | __author__ = "Thibault Dayris" 4 | __copyright__ = "Copyright 2019, Dayris Thibault" 5 | __email__ = "thibault.dayris@gustaveroussy.fr" 6 | __license__ = "MIT" 7 | 8 | import os.path as op 9 | 10 | from snakemake.shell import shell 11 | from snakemake.utils import makedirs 12 | 13 | log = snakemake.log_fmt_shell(stdout=True, stderr=True) 14 | 15 | extra = snakemake.params.get("extra", "") 16 | 17 | # Samtools' threads parameter lists ADDITIONAL threads. 18 | # that is why threads - 1 has to be given to the -@ parameter 19 | threads = "" if snakemake.threads <= 1 else " -@ {} ".format(snakemake.threads - 1) 20 | 21 | makedirs(op.dirname(snakemake.output[0])) 22 | 23 | shell( 24 | "samtools fixmate {extra} {threads}" " {snakemake.input[0]} {snakemake.output[0]}" 25 | ) 26 | -------------------------------------------------------------------------------- /wrappers/bcftools/reheader/wrapper.py: -------------------------------------------------------------------------------- 1 | __author__ = "Jan Forster" 2 | __copyright__ = "Copyright 2020, Jan Forster" 3 | __email__ = "j.forster@dkfz.de" 4 | __license__ = "MIT" 5 | 6 | 7 | from snakemake.shell import shell 8 | 9 | ## Extract arguments 10 | header = snakemake.input.get("header", "") 11 | if header: 12 | header_cmd = "-h " + header 13 | else: 14 | header_cmd = "" 15 | 16 | samples = snakemake.input.get("samples", "") 17 | if samples: 18 | samples_cmd = "-s " + samples 19 | else: 20 | samples_cmd = "" 21 | 22 | extra = snakemake.params.get("extra", "") 23 | view_extra = snakemake.params.get("view_extra", "") 24 | 25 | shell( 26 | "bcftools reheader " 27 | "{extra} " 28 | "{header_cmd} " 29 | "{samples_cmd} " 30 | "{snakemake.input.vcf} " 31 | "| bcftools view " 32 | "{view_extra} " 33 | "> {snakemake.output}" 34 | ) 35 | -------------------------------------------------------------------------------- /pbs_profile/pbs_status.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python3 2 | 3 | import sys 4 | import subprocess 5 | import xml.etree.cElementTree as ET 6 | 7 | jobid = sys.argv[1] 8 | 9 | try: 10 | res = subprocess.run("qstat -f -x {}".format(jobid), check=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, shell=True) 11 | 12 | xmldoc = ET.ElementTree(ET.fromstring(res.stdout.decode())).getroot() 13 | job_state = xmldoc.findall('.//job_state')[0].text 14 | 15 | if job_state == "C": 16 | exit_status = xmldoc.findall('.//exit_status')[0].text 17 | if exit_status == '0': 18 | print("success") 19 | else: 20 | print("failed") 21 | elif job_state == "H": 22 | print("hold") 23 | else: 24 | print("running") 25 | 26 | except (subprocess.CalledProcessError, IndexError, KeyboardInterrupt) as e: 27 | print("failed") 28 | -------------------------------------------------------------------------------- /wrappers/gatk3/realignertargetcreator/meta.yaml: -------------------------------------------------------------------------------- 1 | name: gatk3 RealignerTargetCreator 2 | description: | 3 | Run gatk3 RealignerTargetCreator 4 | authors: 5 | - Patrik Smeds 6 | - Filipe G. Vieira 7 | input: 8 | - bam file 9 | - vcf files 10 | - reference genome 11 | - bed file (optional) 12 | output: 13 | - target intervals 14 | - temp dir (optional) 15 | notes: | 16 | * The `java_opts` param allows for additional arguments to be passed to the java compiler, e.g. "-XX:ParallelGCThreads=10" (memory is automatically inferred from `resources` and temp dir from `output.java_temp`. 17 | * The `extra` param alllows for additional program arguments. 18 | * For more inforamtion see, https://software.broadinstitute.org/gatk/documentation/article?id=11050 19 | * Gatk3.jar is not included in the bioconda package, i.e it need to be added to the conda environment manually. 20 | -------------------------------------------------------------------------------- /wrappers/verifybamid2/wrapper.py: -------------------------------------------------------------------------------- 1 | """Snakemake wrapper for verifybamid2.""" 2 | 3 | __author__ = "Delvin So" 4 | __copyright__ = "Copyright 2020, Delvin So" 5 | __email__ = "delvin.so@sickkids.ca" 6 | __license__ = "MIT" 7 | 8 | import os 9 | from snakemake.shell import shell 10 | log = snakemake.log_fmt_shell(stdout=False, stderr=True) 11 | 12 | out_dir = snakemake.params.get("out_dir") 13 | extra = snakemake.params.get("extra") 14 | svd_prefix = snakemake.params.get("svd_prefix") 15 | 16 | bam = snakemake.input[0] 17 | ref = snakemake.input[1] 18 | 19 | 20 | shell( 21 | "verifybamid2" 22 | " {svd_prefix} " 23 | " --Reference {ref} " 24 | " --Output {out_dir} " 25 | " --BamFile {bam} " 26 | " {extra} " 27 | "{log}" 28 | ) 29 | 30 | shell( 31 | "sed -i 's/{snakemake.wildcards[0]}/{snakemake.wildcards[0]}-{snakemake.wildcards[1]}/g' {snakemake.output.sm}" 32 | ) 33 | --------------------------------------------------------------------------------