├── .github ├── ISSUE_TEMPLATE │ └── bug_report.md └── workflows │ └── ci.yml ├── .gitignore ├── .readthedocs.yml ├── .travis.yml ├── CODE_OF_CONDUCT.md ├── HISTORY.md ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── Vagrantfile ├── artwork ├── bcbio-nextgen.sketch ├── logo.png └── logo.svg ├── bcbio ├── __init__.py ├── bam │ ├── __init__.py │ ├── callable.py │ ├── counts.py │ ├── coverage.py │ ├── cram.py │ ├── fasta.py │ ├── fastq.py │ ├── readstats.py │ ├── ref.py │ ├── skewer.py │ └── trim.py ├── bed │ └── __init__.py ├── broad │ ├── __init__.py │ ├── metrics.py │ └── picardrun.py ├── chipseq │ ├── __init__.py │ ├── antibodies.py │ ├── atac.py │ ├── macs2.py │ └── peaks.py ├── cwl │ ├── __init__.py │ ├── create.py │ ├── cwlutils.py │ ├── defs.py │ ├── hpc.py │ ├── inspect.py │ ├── main.py │ ├── tool.py │ └── workflow.py ├── data │ └── umis │ │ ├── 10x_v2-cb1.txt.gz │ │ ├── 10x_v2-transform.json │ │ ├── dropseq-transform.json │ │ ├── harvard-indrop-v2-cb1.txt.gz │ │ ├── harvard-indrop-v2-cb2.txt.gz │ │ ├── harvard-indrop-v2-transform.json │ │ ├── harvard-indrop-v3-cb1.txt.gz │ │ ├── harvard-indrop-v3-cb2.txt.gz │ │ ├── harvard-indrop-v3-sample_barcodes.txt.gz │ │ ├── harvard-indrop-v3-transform.json │ │ ├── harvard-indrop-v31-cb1.txt.gz │ │ ├── harvard-indrop-v31-cb2.txt.gz │ │ ├── harvard-indrop-v31-transform.json │ │ ├── harvard-scrb-cb1.txt.gz │ │ ├── harvard-scrb-transform.json │ │ ├── icell8-cb1.txt.gz │ │ ├── icell8-transform.json │ │ ├── qiagen_smallRNA_umi-transform.json │ │ ├── qiaseq-upx-384-cb1.txt.gz │ │ ├── qiaseq-upx-384-transform.json │ │ ├── qiaseq-upx-96-cb1.txt.gz │ │ ├── qiaseq-upx-96-transform.json │ │ ├── surecell-cb1.txt.gz │ │ ├── surecell-cb2.txt.gz │ │ ├── surecell-cb3.txt.gz │ │ └── surecell-transform.json ├── distributed │ ├── __init__.py │ ├── clargs.py │ ├── clusterk.py │ ├── ipython.py │ ├── ipythontasks.py │ ├── multi.py │ ├── multitasks.py │ ├── objectstore.py │ ├── prun.py │ ├── resources.py │ ├── runfn.py │ ├── split.py │ └── transaction.py ├── dragen │ ├── __init__.py │ └── dragen.py ├── galaxy │ ├── __init__.py │ ├── api.py │ ├── loc.py │ └── nglims.py ├── graph │ ├── __init__.py │ ├── collectl.py │ └── graph.py ├── heterogeneity │ ├── __init__.py │ ├── bubbletree.py │ ├── chromhacks.py │ ├── loh.py │ ├── phylowgs.py │ └── theta.py ├── hla │ ├── __init__.py │ ├── bwakit.py │ ├── groups.py │ └── optitype.py ├── hmmer │ ├── __init__.py │ └── search.py ├── illumina │ ├── __init__.py │ ├── demultiplex.py │ ├── flowcell.py │ ├── machine.py │ ├── samplesheet.py │ └── transfer.py ├── install.py ├── log │ ├── __init__.py │ └── logbook_zmqpush.py ├── ngsalign │ ├── __init__.py │ ├── alignprep.py │ ├── bbmap.py │ ├── bismark.py │ ├── bowtie.py │ ├── bowtie2.py │ ├── bsmap.py │ ├── bwa.py │ ├── hisat2.py │ ├── minimap2.py │ ├── mosaik.py │ ├── novoalign.py │ ├── postalign.py │ ├── rtg.py │ ├── snap.py │ ├── star.py │ └── tophat.py ├── picard │ ├── __init__.py │ ├── metrics.py │ └── utils.py ├── pipeline │ ├── __init__.py │ ├── alignment.py │ ├── archive.py │ ├── cleanbam.py │ ├── config_utils.py │ ├── datadict.py │ ├── disambiguate │ │ ├── __init__.py │ │ └── run.py │ ├── fastq.py │ ├── genome.py │ ├── main.py │ ├── merge.py │ ├── qcsummary.py │ ├── region.py │ ├── rnaseq.py │ ├── run_info.py │ ├── sample.py │ ├── shared.py │ ├── sra.py │ ├── tools.py │ └── variation.py ├── provenance │ ├── __init__.py │ ├── data.py │ ├── diagnostics.py │ ├── do.py │ ├── profile.py │ ├── programs.py │ ├── system.py │ └── versioncheck.py ├── qc │ ├── __init__.py │ ├── atac.py │ ├── atropos.py │ ├── chipseq.py │ ├── contamination.py │ ├── coverage.py │ ├── damage.py │ ├── fastqc.py │ ├── kraken.py │ ├── multiqc.py │ ├── picard.py │ ├── preseq.py │ ├── qsignature.py │ ├── qualimap.py │ ├── samtools.py │ ├── srna.py │ ├── umi.py │ ├── variant.py │ └── viral.py ├── rnaseq │ ├── __init__.py │ ├── annotate_gtf.py │ ├── arriba.py │ ├── bcbiornaseq.py │ ├── count.py │ ├── cpat.py │ ├── cufflinks.py │ ├── dexseq.py │ ├── ericscript.py │ ├── express.py │ ├── featureCounts.py │ ├── gtf.py │ ├── kallisto.py │ ├── oncofuse.py │ ├── pizzly.py │ ├── qc.py │ ├── rapmap.py │ ├── rsem.py │ ├── sailfish.py │ ├── salmon.py │ ├── singlecellexperiment.py │ ├── spikein.py │ ├── stringtie.py │ ├── umi.py │ └── variation.py ├── scripts │ └── R │ │ ├── bcbio2se.R │ │ └── se2qc.Rmd ├── server │ ├── __init__.py │ ├── background.py │ ├── main.py │ └── run.py ├── setpath.py ├── srna │ ├── __init__.py │ ├── group.py │ ├── mirdeep.py │ ├── mirge.py │ ├── qc.py │ ├── sample.py │ └── umis.py ├── structural │ ├── __init__.py │ ├── annotate.py │ ├── battenberg.py │ ├── cn_mops.py │ ├── cnvkit.py │ ├── convert.py │ ├── delly.py │ ├── gatkcnv.py │ ├── gridss.py │ ├── hydra.py │ ├── lumpy.py │ ├── manta.py │ ├── metasv.py │ ├── pindel.py │ ├── plot.py │ ├── prioritize.py │ ├── purecn.py │ ├── purple.py │ ├── regions.py │ ├── scramble.py │ ├── seq2c.py │ ├── shared.py │ ├── titancna.py │ ├── validate.py │ └── wham.py ├── upload │ ├── __init__.py │ ├── filesystem.py │ ├── galaxy.py │ ├── irods.py │ ├── s3.py │ └── shared.py ├── utils.py ├── variation │ ├── __init__.py │ ├── annotation.py │ ├── bamprep.py │ ├── bedutils.py │ ├── cortex.py │ ├── coverage.py │ ├── damage.py │ ├── deepvariant.py │ ├── effects.py │ ├── ensemble.py │ ├── freebayes.py │ ├── gatk.py │ ├── gatkfilter.py │ ├── gatkjoint.py │ ├── genotype.py │ ├── germline.py │ ├── joint.py │ ├── multi.py │ ├── mutect.py │ ├── mutect2.py │ ├── naming.py │ ├── normalize.py │ ├── octopus.py │ ├── peddy.py │ ├── pisces.py │ ├── platypus.py │ ├── ploidy.py │ ├── population.py │ ├── prioritize.py │ ├── qsnp.py │ ├── realign.py │ ├── recalibrate.py │ ├── samtools.py │ ├── scalpel.py │ ├── sentieon.py │ ├── smcounter2.py │ ├── split.py │ ├── strelka2.py │ ├── validate.py │ ├── validateplot.py │ ├── vardict.py │ ├── varscan.py │ ├── vcfanno.py │ ├── vcfutils.py │ └── vfilter.py ├── wgbsseq │ ├── __init__.py │ ├── align.py │ ├── cpg_caller.py │ ├── deduplication.py │ ├── kits.py │ └── trimming.py └── workflow │ ├── __init__.py │ ├── stormseq.py │ ├── template.py │ └── xprize.py ├── config ├── bcbio_sample.yaml ├── bcbio_system.yaml ├── examples │ ├── HCC2218-sv-getdata.sh │ ├── HCC2218-sv.yaml │ ├── NA12878-ensemble.yaml │ ├── NA12878-exome-methodcmp-getdata.sh │ ├── NA12878-exome-methodcmp.yaml │ ├── NA12878-hg38-validate-getdata.sh │ ├── NA12878-hg38-validate.yaml │ ├── NA12878-illumina.yaml │ ├── NA12878-sv-getdata.sh │ ├── NA12878-sv.yaml │ ├── NA12878-trio-wgs-joint.yaml │ ├── NA12878-trio-wgs-validate-getdata.sh │ ├── NA12878-trio-wgs-validate.yaml │ ├── NA12878.validate.sh │ ├── NA24385-10x-getdata.sh │ ├── NA24385-10x.yaml │ ├── archived │ │ ├── NA12878-trio-sv-getdata.sh │ │ └── NA12878-trio-sv.yaml │ ├── cancer-dream-syn3-getdata.sh │ ├── cancer-dream-syn3.yaml │ ├── cancer-dream-syn4.yaml │ ├── cancer-giab-na12878-na24385-getdata.sh │ ├── cancer-giab-na12878-na24385.yaml │ ├── chip_seq.yaml │ ├── giab-validate-setup.sh │ ├── giab-validate.yaml │ ├── mitochondrial_variants_amplicons.yaml │ ├── rnaseq-seqc-getdata.sh │ ├── rnaseq-seqc.yaml │ ├── rnaseq.variant_calling.yaml │ ├── seqc.csv │ └── somatic_tumor_normal_gatkcnv.yaml ├── galaxy │ └── bcbio │ │ └── variant.xml ├── genomes │ ├── BDGP6-resources.yaml │ ├── GRCh37-resources.yaml │ ├── GRCz10-resources.yaml │ ├── GRCz11-resources.yaml │ ├── Sscrofa11.1-resources.yaml │ ├── TAIR10-resources.yaml │ ├── WBcel235-resources.yaml │ ├── canFam3-resources.yaml │ ├── dm3-resources.yaml │ ├── galGal4-resources.yaml │ ├── hg19-resources.yaml │ ├── hg38-noalt-resources.yaml │ ├── hg38-resources.yaml │ ├── mm10-resources.yaml │ ├── mm9-resources.yaml │ ├── phix-resources.yaml │ ├── pseudomonas_aeruginosa_ucbpp_pa14-resources.yaml │ ├── rn5-resources.yaml │ ├── rn6-resources.yaml │ ├── sacCer3-resources.yaml │ └── xenTro3-resources.yaml ├── teaching │ ├── cancer-syn3-chr6-prep.sh │ └── cancer-syn3-chr6.yaml ├── templates │ ├── bisulfite_seq.yaml │ ├── freebayes-variant.yaml │ ├── gatk-joint-genotyping.yaml │ ├── gatk-variant.yaml │ ├── illumina-chipseq.yaml │ ├── illumina-fastrnaseq.yaml │ ├── illumina-rnaseq.yaml │ ├── illumina-srnaseq.yaml │ ├── indrop-singlecell.yaml │ ├── noalign-variant.yaml │ ├── purecn_pon.yaml │ ├── purecn_ton.yaml │ ├── somatic-duplex-umi.yaml │ ├── somatic-single-umi.yaml │ ├── somatic_tumor_only.yaml │ └── tumor-paired.yaml ├── transfer_info.yaml └── vcfanno │ ├── GRCh37-dbnsfp.conf │ ├── GRCh37-dbscsnv.conf │ ├── GRCh37-gemini.conf │ ├── GRCh37-gemini.lua │ ├── GRCh37-gnomad_genome.conf │ ├── hg38-dbnsfp.conf │ ├── hg38-dbscsnv.conf │ ├── hg38-gemini.conf │ ├── hg38-gemini.lua │ ├── hg38-gnomad_genome.conf │ ├── mm10-gemini.conf │ ├── rnaedit.conf │ ├── rnaedit.lua │ └── somatic.conf ├── docs ├── Makefile ├── conf.py ├── contents │ ├── 3prime_dge.md │ ├── atac.md │ ├── bulk_rnaseq.md │ ├── chip.md │ ├── citations.md │ ├── cloud.md │ ├── configuration.md │ ├── cwl.md │ ├── development.md │ ├── disambiguation.md │ ├── fast_rnaseq.md │ ├── germline_variants.md │ ├── hla_typing.md │ ├── images │ │ ├── banner.png │ │ ├── docker-parallel.png │ │ ├── docker-parallel.svg │ │ ├── parallel-clustertypes.png │ │ ├── parallel-clustertypes.svg │ │ ├── parallel-genome.png │ │ ├── parallel-genome.svg │ │ ├── variant-calling-overview.png │ │ └── variant-calling-overview.svg │ ├── installation.md │ ├── internals.md │ ├── intro.md │ ├── methylation.md │ ├── misc │ │ └── bcbio-smallrna.bib │ ├── outputs.md │ ├── parallel.md │ ├── presentations.md │ ├── purecn.md │ ├── rnaseq_fusions.md │ ├── rnaseq_variants.md │ ├── single_cell.md │ ├── small_rnaseq.md │ ├── somatic_variants.md │ ├── structural_variants.md │ ├── teaching.md │ └── users.md ├── index.md ├── requirements-local.txt ├── requirements.txt └── templates │ └── sidebar-links.html ├── requirements-conda.txt ├── requirements-dev.txt ├── requirements.txt ├── scripts ├── ansible │ ├── README.md │ ├── ansible.cfg │ ├── launch_aws.yaml │ ├── launch_azure.yaml │ └── launch_gce.yaml ├── bcbio_fastq_umi_prep.py ├── bcbio_nextgen.py ├── bcbio_nextgen_install.py ├── bcbio_prepare_samples.py ├── bcbio_setup_genome.py ├── cwl │ └── arvados_bcbio_runtimes.py ├── cwltool2wdl.py └── vagrant.sh ├── setup.cfg ├── setup.py └── tests ├── __init__.py ├── bcbio_vm └── test_docker.py ├── conftest.py ├── data ├── 1_explant │ ├── Hsapiens_Mmusculus_1.fq.gz │ └── Hsapiens_Mmusculus_rep2.fq.gz ├── Harvard-inDrop │ ├── VERSION │ ├── harvard-indrop-v3-b1.txt │ ├── harvard-indrop-v3-b2.txt │ ├── harvard-indrop-v3-sample_barcodes.txt │ ├── klein-v3_R1.fq.gz │ ├── klein-v3_R2.fq.gz │ ├── klein-v3_R3.fq.gz │ ├── klein-v3_R4.fq.gz │ ├── r2-old.gz │ ├── sample-index.txt │ └── transform.json ├── atac │ ├── atac_1.fq │ └── atac_2.fq ├── automated │ ├── coverage_transcripts-bam.bed │ ├── post_process-sample.yaml │ ├── run_info-atacseq.yaml │ ├── run_info-bam.yaml │ ├── run_info-bamclean.yaml │ ├── run_info-cancer.yaml │ ├── run_info-cancer2.yaml │ ├── run_info-cancer3.yaml │ ├── run_info-chipseq.yaml │ ├── run_info-cwl.yaml │ ├── run_info-empty.yaml │ ├── run_info-ericscript.yaml │ ├── run_info-explant.yaml │ ├── run_info-fastrnaseq.yaml │ ├── run_info-fusion.yaml │ ├── run_info-fusion_S3.yaml │ ├── run_info-hisat2.yaml │ ├── run_info-joint.yaml │ ├── run_info-rnaseq-variantcall.yaml │ ├── run_info-rnaseq.yaml │ ├── run_info-scrnaseq.yaml │ ├── run_info-srnaseq_bowtie.yaml │ ├── run_info-srnaseq_star.yaml │ ├── run_info-star.yaml │ ├── run_info-stranded.yaml │ ├── run_info-umi.yaml │ ├── run_info-variantcall.yaml │ ├── run_info-variantcall_S3_1.yaml │ ├── run_info-variantcall_S3_2.yaml │ ├── run_info.yaml │ ├── tool-data │ │ ├── bowtie2_indices.loc │ │ ├── bowtie_indices.loc │ │ ├── bwa_index.loc │ │ ├── mosaik_index.loc │ │ └── sam_fa_indices.loc │ ├── tool_data_table_conf.xml │ ├── universe_wsgi.ini │ ├── variant_regions-bam.bed │ ├── variant_regions-cancer.bed │ ├── variant_regions-priority.bed │ └── variant_regions-variantcall.bed ├── fusion │ ├── input │ │ ├── 1_1_Test1.trimmed.fq.gz │ │ ├── 1_2_Test1.trimmed.fq.gz │ │ └── Test1.nsorted.human.sorted.bam │ └── results │ │ └── TEST_LANE.results.total.tsv ├── genomes │ ├── hg19 │ │ └── bowtie2 │ │ │ ├── hg19.fa │ │ │ └── hg19.fa.fai │ └── mm9 │ │ └── bowtie2 │ │ ├── mm9.fa │ │ └── mm9.fa.fai ├── illumina_samplesheet.csv ├── illumina_samplesheet_fcid_mixed.csv ├── illumina_samplesheet_sampleref_mixed.csv ├── reference_material │ ├── 7_100326_FC6107FAAXX-Test1.vcf.gz │ ├── 7_100326_FC6107FAAXX-Test1.vcf.gz.tbi │ ├── 7_100326_FC6107FAAXX-grade.vcf │ └── background-0-cnvkit.cnn ├── spikeins │ └── spikeins.fa ├── stormseq │ └── stormseq_sample1.cnf ├── structural │ ├── NA12878-hydra.txt │ └── NA12878-hydra.vcf ├── test_chipseq │ ├── Hsapiens_Mmusculus_1.fq │ └── Hsapiens_Mmusculus_1.fq.gz ├── test_fusion │ ├── 1_1.fq.gz │ ├── 1_2.fq.gz │ └── known_fusions.tsv ├── test_srnaseq │ ├── mirqca.fastq │ ├── mirqca.fastq.gz │ └── mirqca_2.fastq ├── test_stranded │ ├── test_1.fq │ ├── test_1.fq.gz │ ├── test_2.fq │ └── test_2.fq.gz └── variants │ ├── S1-variants.vcf │ ├── S2-variants.vcf │ ├── Test1-gatk-haplotype.vcf.gz │ ├── Test1-gatk-haplotype.vcf.gz.tbi │ ├── Test2-gatk-haplotype.vcf.gz │ ├── Test2-gatk-haplotype.vcf.gz.tbi │ ├── TumorOnly.vcf.gz │ └── TumorOnly.vcf.gz.tbi ├── integration ├── __init__.py ├── rnaseq │ ├── __init__.py │ └── test_ericscript.py ├── test_S3_pipelines.py ├── test_SequencingDump.py ├── test_automated_analysis.py └── test_pipeline.py ├── pytest.ini ├── run_tests.sh ├── scripts ├── goofys_logs.sh └── mount.sh └── unit ├── __init__.py ├── conftest.py ├── data.py ├── distributed ├── __init__.py └── test_transaction.py ├── pipeline ├── __init__.py ├── test_datadict.py └── test_rnaseq.py ├── rnaseq ├── __init__.py └── test_ericscript.py ├── test_alignprep.py └── upload ├── __init__.py └── test_upload.py /.github/ISSUE_TEMPLATE/bug_report.md: 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