├── .github └── workflows │ ├── publish.yml │ └── unit_tests.yml ├── .gitignore ├── .pre-commit-config.yaml ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── constants.py ├── docs ├── Makefile ├── _static │ └── css │ │ └── custom.css ├── about.rst ├── bioinformatics.md ├── casestudy │ ├── conversionproblem.md │ ├── conversions_vcf_tabix.png │ └── parsingcwl.md ├── conf.py ├── datatypes │ ├── bai.rst │ ├── bam.rst │ ├── bed.rst │ ├── bedgz.rst │ ├── bedtabix.rst │ ├── boolean.rst │ ├── compressedindexedvcf.rst │ ├── compressedtarfile.rst │ ├── compressedvcf.rst │ ├── crai.rst │ ├── cram.rst │ ├── crampair.rst │ ├── csv.rst │ ├── directory.rst │ ├── double.rst │ ├── fasta.rst │ ├── fastabwa.rst │ ├── fastafai.rst │ ├── fastagz.rst │ ├── fastagzbwa.rst │ ├── fastagzfai.rst │ ├── fastagzwithindexes.rst │ ├── fastawithindexes.rst │ ├── fastdict.rst │ ├── fastgzdict.rst │ ├── fastq.rst │ ├── fastqgz.rst │ ├── file.rst │ ├── filename.rst │ ├── float.rst │ ├── gzip.rst │ ├── htmlfile.rst │ ├── index.rst │ ├── indexedbam.rst │ ├── indexedvcf.rst │ ├── integer.rst │ ├── jsonfile.rst │ ├── kallistoidx.rst │ ├── sam.rst │ ├── stderr.rst │ ├── stdout.rst │ ├── string.rst │ ├── tarfile.rst │ ├── textfile.rst │ ├── tsv.rst │ ├── vcf.rst │ ├── whisperidx.rst │ └── zip.rst ├── development │ ├── contributing.md │ ├── index.rst │ ├── optional.md │ ├── releasing.md │ └── testing.md ├── generationhelpers │ ├── codetool.py │ ├── commandtool.py │ ├── datatype.py │ ├── operators.py │ ├── pipelines.py │ ├── template.py │ ├── utils.py │ └── workflow.py ├── index.rst ├── make.bat ├── motiviations.rst ├── pipelines │ ├── WGSGermlineGATKVariantsOnly_1_3_1.dot │ ├── WGSGermlineGATKVariantsOnly_1_3_1.dot.png │ ├── WGSGermlineGATKVariantsOnly_1_4_0.dot │ ├── WGSGermlineGATKVariantsOnly_1_4_0.dot.png │ ├── WGSGermlineGATK_1_3_1.dot │ ├── WGSGermlineGATK_1_3_1.dot.png │ ├── WGSGermlineGATK_1_4_0.dot │ ├── WGSGermlineGATK_1_4_0.dot.png │ ├── WGSGermlineMultiCallersVariantsOnly_1_3_1.dot │ ├── WGSGermlineMultiCallersVariantsOnly_1_3_1.dot.png │ ├── WGSGermlineMultiCallersVariantsOnly_1_4_0.dot │ ├── WGSGermlineMultiCallersVariantsOnly_1_4_0.dot.png │ ├── WGSGermlineMultiCallers_1_3_1.dot │ ├── WGSGermlineMultiCallers_1_3_1.dot.png │ ├── WGSGermlineMultiCallers_1_4_0.dot │ ├── WGSGermlineMultiCallers_1_4_0.dot.png │ ├── WGSSomaticGATKVariantsOnly_1_3_1.dot │ ├── WGSSomaticGATKVariantsOnly_1_3_1.dot.png │ ├── WGSSomaticGATKVariantsOnly_1_4_0.dot │ ├── WGSSomaticGATKVariantsOnly_1_4_0.dot.png │ ├── WGSSomaticGATK_1_3_1.dot │ ├── WGSSomaticGATK_1_3_1.dot.png │ ├── WGSSomaticGATK_1_4_0.dot │ ├── WGSSomaticGATK_1_4_0.dot.png │ ├── WGSSomaticMultiCallersVariantsOnly_1_3_0.dot │ ├── WGSSomaticMultiCallersVariantsOnly_1_3_0.dot.png │ ├── WGSSomaticMultiCallersVariantsOnly_1_4_0.dot │ ├── WGSSomaticMultiCallersVariantsOnly_1_4_0.dot.png │ ├── WGSSomaticMultiCallers_1_3_0.dot │ ├── WGSSomaticMultiCallers_1_3_0.dot.png │ ├── WGSSomaticMultiCallers_1_4_0.dot │ ├── WGSSomaticMultiCallers_1_4_0.dot.png │ ├── index.rst │ ├── wgsgermlinegatk.rst │ ├── wgsgermlinegatkvariantsonly.rst │ ├── wgsgermlinemulticallers.rst │ ├── wgsgermlinemulticallersvariantsonly.rst │ ├── wgssomaticgatk.rst │ ├── wgssomaticgatkvariantsonly.rst │ ├── wgssomaticmulticallers.rst │ └── wgssomaticmulticallersvariantsonly.rst ├── profiling │ ├── bwamem.md │ ├── cutadapt.md │ ├── gatk_haplotypecaller.md │ └── optimise.md ├── references │ ├── callcaching.md │ ├── cli.md │ ├── commandtool.rst │ ├── conditionals.rst │ ├── configuration.rst │ ├── cwl.rst │ ├── dynamicworkflows.rst │ ├── engines.rst │ ├── errors.md │ ├── expressions.rst │ ├── faq.md │ ├── index.rst │ ├── listoperators.rst │ ├── prepare.rst │ ├── resources.md │ ├── scattering.rst │ ├── secondaryfiles.rst │ ├── selectors.rst │ ├── shed.rst │ ├── tools │ │ ├── codetool.rst │ │ └── pythontool.rst │ ├── types.rst │ ├── unittest.rst │ ├── updating.md │ ├── wdl.rst │ └── workflow.rst ├── regeneratedocumentation.py ├── requirements.txt ├── resources │ ├── bakecookie-wf.png │ ├── bakecookie.gliffy │ ├── optimisation │ │ ├── bwamem-cost.pdf │ │ ├── bwamem-total.pdf │ │ ├── cutadapt-cputime.svg │ │ └── cutadapt-time-taken.pdf │ ├── requirements.md │ ├── run-unit-tests.png │ └── simple.png ├── templates │ ├── index.rst │ ├── local.rst │ ├── molpath.rst │ ├── pawsey.rst │ ├── pbs_singularity.rst │ ├── pmac.rst │ ├── singularity.rst │ ├── slurm_singularity.rst │ ├── spartan.rst │ └── wehi.rst ├── tools │ ├── bioinformatics │ │ ├── arriba │ │ │ ├── arriba.rst │ │ │ ├── arriba_1.1.0.rst │ │ │ ├── arriba_1.2.0.rst │ │ │ └── index.rst │ │ ├── bcftools │ │ │ ├── bcftoolsannotate.rst │ │ │ ├── bcftoolsannotate_v1.5.rst │ │ │ ├── bcftoolsannotate_v1.9.rst │ │ │ ├── bcftoolsconcat.rst │ │ │ ├── bcftoolsconcat_v1.9.rst │ │ │ ├── bcftoolsindex.rst │ │ │ ├── bcftoolsindex_v1.9.rst │ │ │ ├── bcftoolsnorm.rst │ │ │ ├── bcftoolsnorm_v1.5.rst │ │ │ ├── bcftoolsnorm_v1.9.rst │ │ │ ├── bcftoolssort.rst │ │ │ ├── bcftoolssort_v1.9.rst │ │ │ ├── bcftoolsview.rst │ │ │ ├── bcftoolsview_v1.5.rst │ │ │ ├── bcftoolsview_v1.9.rst │ │ │ └── index.rst │ │ ├── bedtools │ │ │ ├── bedtoolscoveragebed.rst │ │ │ ├── bedtoolscoveragebed_v2.29.2.rst │ │ │ ├── bedtoolsgenomecoveragebed.rst │ │ │ ├── bedtoolsgenomecoveragebed_v2.29.2.rst │ │ │ ├── bedtoolsintersectbed.rst │ │ │ ├── bedtoolsintersectbed_v2.29.2.rst │ │ │ └── index.rst │ │ ├── biobambam │ │ │ ├── bamsormadup.rst │ │ │ ├── bamsormadup_2.0.87.rst │ │ │ └── index.rst │ │ ├── broad institute │ │ │ ├── gatk3depthofcoverage.rst │ │ │ ├── gatk3depthofcoverage_3.8-0.rst │ │ │ ├── gatk3depthofcoverage_3.8-1.rst │ │ │ └── index.rst │ │ ├── bwa │ │ │ ├── bwaindex.rst │ │ │ ├── bwaindex_v0.7.15.rst │ │ │ ├── bwamem.rst │ │ │ ├── bwamem_v0.7.15.rst │ │ │ └── index.rst │ │ ├── cellranger │ │ │ ├── cellrangermkfastq.rst │ │ │ ├── cellrangermkfastq_v3.0.2.rst │ │ │ └── index.rst │ │ ├── cold spring harbor laboratory │ │ │ ├── index.rst │ │ │ ├── star_alignreads.rst │ │ │ ├── star_alignreads_v2.5.3a.rst │ │ │ ├── star_alignreads_v2.7.1a.rst │ │ │ ├── star_alignreads_v2.7.5c.rst │ │ │ ├── star_genomegenerate.rst │ │ │ ├── star_genomegenerate_v2.5.3a.rst │ │ │ ├── star_genomegenerate_v2.7.1a.rst │ │ │ └── star_genomegenerate_v2.7.5c.rst │ │ ├── common │ │ │ ├── BwaAligner_1_0_0.dot │ │ │ ├── BwaAligner_1_0_0.dot.png │ │ │ ├── GATKBaseRecalBQSRWorkflow_4_1_2.dot │ │ │ ├── GATKBaseRecalBQSRWorkflow_4_1_2.dot.png │ │ │ ├── GATKBaseRecalBQSRWorkflow_4_1_3.dot │ │ │ ├── GATKBaseRecalBQSRWorkflow_4_1_3.dot.png │ │ │ ├── IndexFasta_1_0_0.dot │ │ │ ├── IndexFasta_1_0_0.dot.png │ │ │ ├── bwaaligner.rst │ │ │ ├── bwaaligner_1.0.0.rst │ │ │ ├── bwamemsamtoolsview.rst │ │ │ ├── bwamemsamtoolsview_0.7.17%7c1.9.rst │ │ │ ├── concatstrelkasomaticvcf.rst │ │ │ ├── concatstrelkasomaticvcf_0.1.16.rst │ │ │ ├── filtervardictsomaticvcf.rst │ │ │ ├── filtervardictsomaticvcf_v1.9.rst │ │ │ ├── gatkbaserecalbqsrworkflow.rst │ │ │ ├── gatkbaserecalbqsrworkflow_4.1.2.rst │ │ │ ├── gatkbaserecalbqsrworkflow_4.1.3.rst │ │ │ ├── index.rst │ │ │ ├── indexfasta.rst │ │ │ ├── indexfasta_1.0.0.rst │ │ │ ├── mergeAndMarkBams_4_0_12.dot │ │ │ ├── mergeAndMarkBams_4_0_12.dot.png │ │ │ ├── mergeAndMarkBams_4_1_2.dot │ │ │ ├── mergeAndMarkBams_4_1_2.dot.png │ │ │ ├── mergeAndMarkBams_4_1_3.dot │ │ │ ├── mergeAndMarkBams_4_1_3.dot.png │ │ │ ├── mergeandmarkbams.rst │ │ │ ├── mergeandmarkbams_4.0.12.rst │ │ │ ├── mergeandmarkbams_4.1.2.rst │ │ │ └── mergeandmarkbams_4.1.3.rst │ │ ├── cutadapt │ │ │ ├── cutadapt.rst │ │ │ ├── cutadapt_1.18.rst │ │ │ ├── cutadapt_2.1.rst │ │ │ ├── cutadapt_2.4.rst │ │ │ ├── cutadapt_2.5.rst │ │ │ ├── cutadapt_2.6.rst │ │ │ └── index.rst │ │ ├── dawson labs │ │ │ ├── FreeBayesSomaticWorkflowCram_0_1_1.dot │ │ │ ├── FreeBayesSomaticWorkflowCram_0_1_1.dot.png │ │ │ ├── FreeBayesSomaticWorkflow_0_1_1.dot │ │ │ ├── FreeBayesSomaticWorkflow_0_1_1.dot.png │ │ │ ├── Mutect2JointSomaticWorkflowCram_0_1_1.dot │ │ │ ├── Mutect2JointSomaticWorkflowCram_0_1_1.dot.png │ │ │ ├── Mutect2JointSomaticWorkflow_0_1_1.dot │ │ │ ├── Mutect2JointSomaticWorkflow_0_1_1.dot.png │ │ │ ├── Strelka2PassWorkflowCram_0_2.dot │ │ │ ├── Strelka2PassWorkflowCram_0_2.dot.png │ │ │ ├── Strelka2PassWorkflow_0_2.dot │ │ │ ├── Strelka2PassWorkflow_0_2.dot.png │ │ │ ├── callsomaticfreebayes.rst │ │ │ ├── callsomaticfreebayes_0.1.8.rst │ │ │ ├── createcallregions.rst │ │ │ ├── createcallregions_v0.1.0.rst │ │ │ ├── freebayessomaticworkflow.rst │ │ │ ├── freebayessomaticworkflow_0.1.1.rst │ │ │ ├── freebayessomaticworkflowcram.rst │ │ │ ├── freebayessomaticworkflowcram_0.1.1.rst │ │ │ ├── index.rst │ │ │ ├── mutect2jointsomaticworkflow.rst │ │ │ ├── mutect2jointsomaticworkflow_0.1.1.rst │ │ │ ├── mutect2jointsomaticworkflowcram.rst │ │ │ ├── mutect2jointsomaticworkflowcram_0.1.1.rst │ │ │ ├── refilterstrelka2calls.rst │ │ │ ├── refilterstrelka2calls_0.1.8.rst │ │ │ ├── strelka2passworkflow.rst │ │ │ ├── strelka2passworkflow_0.2.rst │ │ │ ├── strelka2passworkflowcram.rst │ │ │ └── strelka2passworkflowcram_0.2.rst │ │ ├── ekg │ │ │ ├── index.rst │ │ │ ├── vcfallelicprimitives.rst │ │ │ ├── vcfallelicprimitives_v1.0.1.rst │ │ │ ├── vcfcombine.rst │ │ │ ├── vcfcombine_v1.0.1.rst │ │ │ ├── vcffilter.rst │ │ │ ├── vcffilter_v1.0.1.rst │ │ │ ├── vcffixup.rst │ │ │ ├── vcffixup_v1.0.1.rst │ │ │ ├── vcflength.rst │ │ │ ├── vcflength_v1.0.1.rst │ │ │ ├── vcfrandomsample.rst │ │ │ ├── vcfrandomsample_v1.0.1.rst │ │ │ ├── vcfroc.rst │ │ │ ├── vcfroc_v1.0.1.rst │ │ │ ├── vcfstreamsort.rst │ │ │ ├── vcfstreamsort_v1.0.1.rst │ │ │ ├── vcfuniq.rst │ │ │ ├── vcfuniq_v1.0.1.rst │ │ │ ├── vcfuniqalleles.rst │ │ │ └── vcfuniqalleles_v1.0.1.rst │ │ ├── ensembl │ │ │ ├── filtervep.rst │ │ │ ├── filtervep_98.3.rst │ │ │ ├── index.rst │ │ │ ├── vep_cache.rst │ │ │ ├── vep_cache_98.3.rst │ │ │ ├── vep_database.rst │ │ │ └── vep_database_98.3.rst │ │ ├── erik garrison │ │ │ ├── freebayes.rst │ │ │ ├── freebayes_1.2.rst │ │ │ ├── freebayes_1.3.1.rst │ │ │ ├── freebayes_cram.rst │ │ │ ├── freebayes_cram_1.3.1.rst │ │ │ └── index.rst │ │ ├── facets │ │ │ ├── facetssnppileup.rst │ │ │ ├── facetssnppileup_0.5.14-2.rst │ │ │ ├── facetssnppileup_0.5.14.1.rst │ │ │ ├── facetssnppileup_0.5.14.rst │ │ │ └── index.rst │ │ ├── fastqc │ │ │ ├── fastqc.rst │ │ │ ├── fastqc_single.rst │ │ │ ├── fastqc_single_scattered.rst │ │ │ ├── fastqc_single_scattered_v0.11.8.rst │ │ │ ├── fastqc_single_scattered_v0_11_8.dot │ │ │ ├── fastqc_single_scattered_v0_11_8.dot.png │ │ │ ├── fastqc_single_v0.11.5.rst │ │ │ ├── fastqc_single_v0.11.8.rst │ │ │ ├── fastqc_v0.11.5.rst │ │ │ ├── fastqc_v0.11.8.rst │ │ │ └── index.rst │ │ ├── gatk4 │ │ │ ├── gatk4applybqsr.rst │ │ │ ├── gatk4applybqsr_4.0.12.0.rst │ │ │ ├── gatk4applybqsr_4.1.2.0.rst │ │ │ ├── gatk4applybqsr_4.1.3.0.rst │ │ │ ├── gatk4applybqsr_4.1.4.0.rst │ │ │ ├── gatk4baserecalibrator.rst │ │ │ ├── gatk4baserecalibrator_4.0.12.0.rst │ │ │ ├── gatk4baserecalibrator_4.1.2.0.rst │ │ │ ├── gatk4baserecalibrator_4.1.3.0.rst │ │ │ ├── gatk4baserecalibrator_4.1.4.0.rst │ │ │ ├── gatk4calculatecontamination.rst │ │ │ ├── gatk4calculatecontamination_4.1.2.0.rst │ │ │ ├── gatk4calculatecontamination_4.1.3.0.rst │ │ │ ├── gatk4calculatecontamination_4.1.4.0.rst │ │ │ ├── gatk4calculatecontamination_4.1.6.0.rst │ │ │ ├── gatk4calculatecontamination_4.1.7.0.rst │ │ │ ├── gatk4calculatecontamination_4.1.8.1.rst │ │ │ ├── gatk4collectinsertsizemetrics.rst │ │ │ ├── gatk4collectinsertsizemetrics_4.0.12.0.rst │ │ │ ├── gatk4collectinsertsizemetrics_4.1.2.0.rst │ │ │ ├── gatk4collectinsertsizemetrics_4.1.3.0.rst │ │ │ ├── gatk4collectinsertsizemetrics_4.1.4.0.rst │ │ │ ├── gatk4createsequencedictionary.rst │ │ │ ├── gatk4createsequencedictionary_4.1.2.0.rst │ │ │ ├── gatk4createsequencedictionary_4.1.3.0.rst │ │ │ ├── gatk4createsequencedictionary_4.1.4.0.rst │ │ │ ├── gatk4depthofcoverage.rst │ │ │ ├── gatk4depthofcoverage_4.1.6.0.rst │ │ │ ├── gatk4fastqtosam.rst │ │ │ ├── gatk4fastqtosam_4.0.12.0.rst │ │ │ ├── gatk4fastqtosam_4.1.2.0.rst │ │ │ ├── gatk4fastqtosam_4.1.3.0.rst │ │ │ ├── gatk4fastqtosam_4.1.4.1.rst │ │ │ ├── gatk4filtermutectcalls.rst │ │ │ ├── gatk4filtermutectcalls_4.1.2.0.rst │ │ │ ├── gatk4filtermutectcalls_4.1.3.0.rst │ │ │ ├── gatk4filtermutectcalls_4.1.4.0.rst │ │ │ ├── gatk4filtermutectcalls_4.1.6.0.rst │ │ │ ├── gatk4filtermutectcalls_4.1.7.0.rst │ │ │ ├── gatk4filtermutectcalls_4.1.8.1.rst │ │ │ ├── gatk4gatherbamfiles.rst │ │ │ ├── gatk4gatherbamfiles_4.1.2.0.rst │ │ │ ├── gatk4gatherbamfiles_4.1.3.0.rst │ │ │ ├── gatk4gatherbamfiles_4.1.4.0.rst │ │ │ ├── gatk4gatherbqsrreports.rst │ │ │ ├── gatk4gatherbqsrreports_4.0.12.0.rst │ │ │ ├── gatk4gatherbqsrreports_4.1.2.0.rst │ │ │ ├── gatk4gatherbqsrreports_4.1.3.0.rst │ │ │ ├── gatk4gatherbqsrreports_4.1.4.0.rst │ │ │ ├── gatk4gathervcfs.rst │ │ │ ├── gatk4gathervcfs_4.0.12.0.rst │ │ │ ├── gatk4gathervcfs_4.1.2.0.rst │ │ │ ├── gatk4gathervcfs_4.1.3.0.rst │ │ │ ├── gatk4gathervcfs_4.1.4.0.rst │ │ │ ├── gatk4genotypeconcordance.rst │ │ │ ├── gatk4genotypeconcordance_4.0.12.0.rst │ │ │ ├── gatk4genotypeconcordance_4.1.2.0.rst │ │ │ ├── gatk4genotypeconcordance_4.1.3.0.rst │ │ │ ├── gatk4genotypeconcordance_4.1.4.0.rst │ │ │ ├── gatk4getpileupsummaries.rst │ │ │ ├── gatk4getpileupsummaries_4.1.2.0.rst │ │ │ ├── gatk4getpileupsummaries_4.1.3.0.rst │ │ │ ├── gatk4getpileupsummaries_4.1.4.0.rst │ │ │ ├── gatk4getpileupsummaries_4.1.6.0.rst │ │ │ ├── gatk4getpileupsummaries_4.1.7.0.rst │ │ │ ├── gatk4getpileupsummaries_4.1.8.1.rst │ │ │ ├── gatk4getpileupsummaries_cram.rst │ │ │ ├── gatk4getpileupsummaries_cram_4.1.2.0.rst │ │ │ ├── gatk4getpileupsummaries_cram_4.1.3.0.rst │ │ │ ├── gatk4getpileupsummaries_cram_4.1.4.0.rst │ │ │ ├── gatk4getpileupsummaries_cram_4.1.6.0.rst │ │ │ ├── gatk4getpileupsummaries_cram_4.1.7.0.rst │ │ │ ├── gatk4getpileupsummaries_cram_4.1.8.1.rst │ │ │ ├── gatk4haplotypecaller.rst │ │ │ ├── gatk4haplotypecaller_4.0.12.0.rst │ │ │ ├── gatk4haplotypecaller_4.1.2.0.rst │ │ │ ├── gatk4haplotypecaller_4.1.3.0.rst │ │ │ ├── gatk4haplotypecaller_4.1.4.0.rst │ │ │ ├── gatk4haplotypecaller_4.1.6.0.rst │ │ │ ├── gatk4haplotypecaller_4.1.7.0.rst │ │ │ ├── gatk4haplotypecaller_4.1.8.1.rst │ │ │ ├── gatk4learnreadorientationmodel.rst │ │ │ ├── gatk4learnreadorientationmodel_4.1.2.0.rst │ │ │ ├── gatk4learnreadorientationmodel_4.1.3.0.rst │ │ │ ├── gatk4learnreadorientationmodel_4.1.4.0.rst │ │ │ ├── gatk4learnreadorientationmodel_4.1.6.0.rst │ │ │ ├── gatk4learnreadorientationmodel_4.1.7.0.rst │ │ │ ├── gatk4learnreadorientationmodel_4.1.8.1.rst │ │ │ ├── gatk4markduplicates.rst │ │ │ ├── gatk4markduplicates_4.0.12.0.rst │ │ │ ├── gatk4markduplicates_4.1.2.0.rst │ │ │ ├── gatk4markduplicates_4.1.3.0.rst │ │ │ ├── gatk4markduplicates_4.1.4.0.rst │ │ │ ├── gatk4mergebamalignment.rst │ │ │ ├── gatk4mergebamalignment_4.0.12.0.rst │ │ │ ├── gatk4mergebamalignment_4.1.2.0.rst │ │ │ ├── gatk4mergebamalignment_4.1.3.0.rst │ │ │ ├── gatk4mergebamalignment_4.1.4.1.rst │ │ │ ├── gatk4mergemutectstats.rst │ │ │ ├── gatk4mergemutectstats_4.1.2.0.rst │ │ │ ├── gatk4mergemutectstats_4.1.3.0.rst │ │ │ ├── gatk4mergemutectstats_4.1.4.0.rst │ │ │ ├── gatk4mergemutectstats_4.1.6.0.rst │ │ │ ├── gatk4mergemutectstats_4.1.7.0.rst │ │ │ ├── gatk4mergemutectstats_4.1.8.1.rst │ │ │ ├── gatk4mergesamfiles.rst │ │ │ ├── gatk4mergesamfiles_4.0.12.0.rst │ │ │ ├── gatk4mergesamfiles_4.1.2.0.rst │ │ │ ├── gatk4mergesamfiles_4.1.3.0.rst │ │ │ ├── gatk4mergesamfiles_4.1.4.0.rst │ │ │ ├── gatk4mutect2.rst │ │ │ ├── gatk4mutect2_4.0.12.0.rst │ │ │ ├── gatk4mutect2_4.1.2.0.rst │ │ │ ├── gatk4mutect2_4.1.3.0.rst │ │ │ ├── gatk4mutect2_4.1.4.0.rst │ │ │ ├── gatk4mutect2_4.1.6.0.rst │ │ │ ├── gatk4mutect2_4.1.7.0.rst │ │ │ ├── gatk4mutect2_4.1.8.1.rst │ │ │ ├── gatk4mutect2_cram.rst │ │ │ ├── gatk4mutect2_cram_4.1.2.0.rst │ │ │ ├── gatk4mutect2_cram_4.1.3.0.rst │ │ │ ├── gatk4mutect2_cram_4.1.4.0.rst │ │ │ ├── gatk4mutect2_cram_4.1.6.0.rst │ │ │ ├── gatk4mutect2_cram_4.1.7.0.rst │ │ │ ├── gatk4mutect2_cram_4.1.8.1.rst │ │ │ ├── gatk4printreads.rst │ │ │ ├── gatk4printreads_4.0.12.0.rst │ │ │ ├── gatk4printreads_4.1.2.0.rst │ │ │ ├── gatk4printreads_4.1.3.0.rst │ │ │ ├── gatk4printreads_4.1.4.0.rst │ │ │ ├── gatk4selectvariants.rst │ │ │ ├── gatk4selectvariants_4.0.12.0.rst │ │ │ ├── gatk4selectvariants_4.1.2.0.rst │ │ │ ├── gatk4selectvariants_4.1.3.0.rst │ │ │ ├── gatk4selectvariants_4.1.4.0.rst │ │ │ ├── gatk4setnmmdanduqtags.rst │ │ │ ├── gatk4setnmmdanduqtags_4.1.3.0.rst │ │ │ ├── gatk4setnmmdanduqtags_4.1.4.0.rst │ │ │ ├── gatk4sortsam.rst │ │ │ ├── gatk4sortsam_4.0.12.0.rst │ │ │ ├── gatk4sortsam_4.1.2.0.rst │ │ │ ├── gatk4sortsam_4.1.3.0.rst │ │ │ ├── gatk4sortsam_4.1.4.0.rst │ │ │ ├── gatk4splitreads.rst │ │ │ ├── gatk4splitreads_4.1.2.0.rst │ │ │ ├── gatk4splitreads_4.1.3.0.rst │ │ │ ├── gatk4splitreads_4.1.4.0.rst │ │ │ ├── gatk4variantfiltration.rst │ │ │ ├── gatk4variantfiltration_4.0.12.0.rst │ │ │ ├── gatk4variantfiltration_4.1.2.0.rst │ │ │ ├── gatk4variantfiltration_4.1.3.0.rst │ │ │ ├── gatk4variantfiltration_4.1.4.0.rst │ │ │ ├── gatkaddorreplacereadgroups.rst │ │ │ ├── gatkaddorreplacereadgroups_4.0.12.0.rst │ │ │ ├── gatkaddorreplacereadgroups_4.1.2.0.rst │ │ │ ├── gatkaddorreplacereadgroups_4.1.3.0.rst │ │ │ ├── gatkaddorreplacereadgroups_4.1.4.0.rst │ │ │ ├── gatkreordersam.rst │ │ │ ├── gatkreordersam_4.1.4.0.rst │ │ │ ├── gatksplitncigarreads.rst │ │ │ ├── gatksplitncigarreads_4.0.12.0.rst │ │ │ ├── gatksplitncigarreads_4.1.2.0.rst │ │ │ ├── gatksplitncigarreads_4.1.3.0.rst │ │ │ ├── gatksplitncigarreads_4.1.4.0.rst │ │ │ └── index.rst │ │ ├── htslib │ │ │ ├── bgzip.rst │ │ │ ├── bgzip_1.2.1.rst │ │ │ ├── bgzip_1.9.rst │ │ │ ├── index.rst │ │ │ ├── tabix.rst │ │ │ ├── tabix_1.2.1.rst │ │ │ └── tabix_1.9.rst │ │ ├── igvtools │ │ │ ├── igvtoolsindexfeatures.rst │ │ │ ├── igvtoolsindexfeatures_2.5.3.rst │ │ │ └── index.rst │ │ ├── illumina │ │ │ ├── bcl2fastq.rst │ │ │ ├── bcl2fastq_2.20.0.rst │ │ │ ├── happy_validator.rst │ │ │ ├── happy_validator_v0.3.9.rst │ │ │ ├── index.rst │ │ │ ├── manta.rst │ │ │ ├── manta_1.4.0.rst │ │ │ ├── manta_1.5.0.rst │ │ │ ├── manta_cram.rst │ │ │ ├── manta_cram_1.4.0.rst │ │ │ ├── manta_cram_1.5.0.rst │ │ │ ├── strelka_germline.rst │ │ │ ├── strelka_germline_2.9.10.rst │ │ │ ├── strelka_germline_2.9.9.rst │ │ │ ├── strelka_somatic.rst │ │ │ ├── strelka_somatic_2.9.10.rst │ │ │ ├── strelka_somatic_2.9.9.rst │ │ │ ├── strelka_somatic_cram.rst │ │ │ ├── strelka_somatic_cram_2.9.10.rst │ │ │ └── strelka_somatic_cram_2.9.9.rst │ │ ├── index.rst │ │ ├── io_lib │ │ │ ├── index.rst │ │ │ ├── scramble.rst │ │ │ └── scramble_1.14.12.rst │ │ ├── kallisto │ │ │ ├── index.rst │ │ │ ├── kallistoindex.rst │ │ │ ├── kallistoindex_v0.46.2.rst │ │ │ ├── kallistoquant.rst │ │ │ └── kallistoquant_v0.46.2.rst │ │ ├── multiqc │ │ │ ├── index.rst │ │ │ ├── multiqc.rst │ │ │ └── multiqc_v1.7.rst │ │ ├── oncopipe │ │ │ ├── OncopipeSamplePreparation_v0_1_0.dot │ │ │ ├── OncopipeSamplePreparation_v0_1_0.dot.png │ │ │ ├── index.rst │ │ │ ├── oncopipe.rst │ │ │ ├── oncopipe_v0.1.0.rst │ │ │ ├── oncopipe_v0_1_0.dot │ │ │ ├── oncopipe_v0_1_0.dot.png │ │ │ ├── oncopipesamplepreparation.rst │ │ │ └── oncopipesamplepreparation_v0.1.0.rst │ │ ├── oshlack │ │ │ ├── allsorts.rst │ │ │ ├── allsorts_v0.1.0.rst │ │ │ └── index.rst │ │ ├── papenfuss labs │ │ │ ├── gridss.rst │ │ │ ├── gridss_v2.2.3.rst │ │ │ ├── gridss_v2.4.0.rst │ │ │ ├── gridss_v2.5.1-dev.rst │ │ │ ├── gridss_v2.6.2.rst │ │ │ ├── gridss_v2.9.4.rst │ │ │ └── index.rst │ │ ├── peter maccallum cancer centre │ │ │ ├── AddBamStatsGermline_v0_1_0.dot │ │ │ ├── AddBamStatsGermline_v0_1_0.dot.png │ │ │ ├── AddBamStatsSomatic_v0_1_0.dot │ │ │ ├── AddBamStatsSomatic_v0_1_0.dot.png │ │ │ ├── AnnotateDepthOfCoverage_v0_1_0.dot │ │ │ ├── AnnotateDepthOfCoverage_v0_1_0.dot.png │ │ │ ├── MolpathGermlineWorkflow_v1_0_0.dot │ │ │ ├── MolpathGermlineWorkflow_v1_0_0.dot.png │ │ │ ├── MolpathTumorOnlyWorkflow_v1_0_0.dot │ │ │ ├── MolpathTumorOnlyWorkflow_v1_0_0.dot.png │ │ │ ├── PerformanceSummaryGenome_v0_1_0.dot │ │ │ ├── PerformanceSummaryGenome_v0_1_0.dot.png │ │ │ ├── PerformanceSummaryTargeted_v0_1_0.dot │ │ │ ├── PerformanceSummaryTargeted_v0_1_0.dot.png │ │ │ ├── addbamstats.rst │ │ │ ├── addbamstats_0.0.7.rst │ │ │ ├── addbamstatsgermline.rst │ │ │ ├── addbamstatsgermline_v0.1.0.rst │ │ │ ├── addbamstatssomatic.rst │ │ │ ├── addbamstatssomatic_v0.1.0.rst │ │ │ ├── addsymtodepthofcoverage.rst │ │ │ ├── addsymtodepthofcoverage_0.0.7.rst │ │ │ ├── annotatedepthofcoverage.rst │ │ │ ├── annotatedepthofcoverage_v0.1.0.rst │ │ │ ├── combinevariants.rst │ │ │ ├── combinevariants_0.0.8.rst │ │ │ ├── extractstrelkasomaticaddp.rst │ │ │ ├── extractstrelkasomaticaddp_0.1.0.rst │ │ │ ├── extractstrelkasomaticaddp_0.1.1.rst │ │ │ ├── genecoveragepersample.rst │ │ │ ├── genecoveragepersample_0.0.7.rst │ │ │ ├── genecoveragepersample_0.0.8.rst │ │ │ ├── generategenomefileforbedtoolscoverage.rst │ │ │ ├── generategenomefileforbedtoolscoverage_v0.1.0.rst │ │ │ ├── generateintervalsbychromosome.rst │ │ │ ├── generateintervalsbychromosome_v0.1.0.rst │ │ │ ├── generatevardictheaderlines.rst │ │ │ ├── generatevardictheaderlines_v0.1.0.rst │ │ │ ├── index.rst │ │ │ ├── molpathgermlineworkflow.rst │ │ │ ├── molpathgermlineworkflow_v1.0.0.rst │ │ │ ├── molpathtumoronlyworkflow.rst │ │ │ ├── molpathtumoronlyworkflow_v1.0.0.rst │ │ │ ├── parsefastqcadaptors.rst │ │ │ ├── parsefastqcadaptors_v0.1.0.rst │ │ │ ├── performancesummary.rst │ │ │ ├── performancesummary_0.0.7.rst │ │ │ ├── performancesummarygenome.rst │ │ │ ├── performancesummarygenome_v0.1.0.rst │ │ │ ├── performancesummarytargeted.rst │ │ │ ├── performancesummarytargeted_v0.1.0.rst │ │ │ ├── prepareallsortsinput.rst │ │ │ ├── prepareallsortsinput_v0.1.0.rst │ │ │ ├── splitmultiallele.rst │ │ │ ├── splitmultiallele_v0.5772.rst │ │ │ ├── splitmultiallelenormalisevcf.rst │ │ │ ├── splitmultiallelenormalisevcf_v0.5772.rst │ │ │ ├── trimiupac.rst │ │ │ ├── trimiupac_0.0.4.rst │ │ │ └── trimiupac_0.0.5.rst │ │ ├── samtools │ │ │ ├── index.rst │ │ │ ├── samtoolsfaidx.rst │ │ │ ├── samtoolsfaidx_1.7.0.rst │ │ │ ├── samtoolsfaidx_1.9.0.rst │ │ │ ├── samtoolsflagstat.rst │ │ │ ├── samtoolsflagstat_1.7.0.rst │ │ │ ├── samtoolsflagstat_1.9.0.rst │ │ │ ├── samtoolsindex.rst │ │ │ ├── samtoolsindex_1.7.0.rst │ │ │ ├── samtoolsindex_1.9.0.rst │ │ │ ├── samtoolsmpileup.rst │ │ │ ├── samtoolsmpileup_1.7.0.rst │ │ │ ├── samtoolsmpileup_1.9.0.rst │ │ │ ├── samtoolssort.rst │ │ │ ├── samtoolssort_1.7.0.rst │ │ │ ├── samtoolssort_1.9.0.rst │ │ │ ├── samtoolsview.rst │ │ │ ├── samtoolsview_1.7.0.rst │ │ │ └── samtoolsview_1.9.0.rst │ │ ├── sequenza │ │ │ ├── index.rst │ │ │ ├── seqzbam2seqz.rst │ │ │ ├── seqzbam2seqz_2.2.0.9000.rst │ │ │ ├── seqzbam2seqz_3.0.0.rst │ │ │ ├── seqzbinning.rst │ │ │ ├── seqzbinning_2.2.0.9000.rst │ │ │ └── seqzbinning_3.0.0.rst │ │ ├── subread │ │ │ ├── featurecounts.rst │ │ │ ├── featurecounts_2.0.1.rst │ │ │ └── index.rst │ │ ├── ucsf │ │ │ ├── cnvkit.rst │ │ │ ├── cnvkit_0.9.6.rst │ │ │ └── index.rst │ │ ├── usadel lab │ │ │ ├── index.rst │ │ │ ├── trimmomaticpairedend.rst │ │ │ ├── trimmomaticpairedend_0.35.rst │ │ │ ├── trimmomaticsingleend.rst │ │ │ └── trimmomaticsingleend_0.35.rst │ │ ├── vardict │ │ │ ├── index.rst │ │ │ ├── vardict_germline.rst │ │ │ ├── vardict_germline_1.5.6.rst │ │ │ ├── vardict_germline_1.5.7.rst │ │ │ ├── vardict_germline_1.5.8.rst │ │ │ ├── vardict_germline_1.6.0.rst │ │ │ ├── vardict_germline_1.7.0.rst │ │ │ ├── vardict_somatic.rst │ │ │ ├── vardict_somatic_1.5.6.rst │ │ │ ├── vardict_somatic_1.5.7.rst │ │ │ ├── vardict_somatic_1.5.8.rst │ │ │ ├── vardict_somatic_1.6.0.rst │ │ │ └── vardict_somatic_1.7.0.rst │ │ ├── variant callers │ │ │ ├── GATK4_GermlineVariantCaller_4_0_12_0.dot │ │ │ ├── GATK4_GermlineVariantCaller_4_0_12_0.dot.png │ │ │ ├── GATK4_GermlineVariantCaller_4_1_3_0.dot │ │ │ ├── GATK4_GermlineVariantCaller_4_1_3_0.dot.png │ │ │ ├── GATK4_SomaticVariantCallerTumorOnlyTargeted_v0_1_1.dot │ │ │ ├── GATK4_SomaticVariantCallerTumorOnlyTargeted_v0_1_1.dot.png │ │ │ ├── GATK4_SomaticVariantCaller_4_0_12_0.dot │ │ │ ├── GATK4_SomaticVariantCaller_4_0_12_0.dot.png │ │ │ ├── GATK4_SomaticVariantCaller_4_1_3_0.dot │ │ │ ├── GATK4_SomaticVariantCaller_4_1_3_0.dot.png │ │ │ ├── gatk4_germlinevariantcaller.rst │ │ │ ├── gatk4_germlinevariantcaller_4.0.12.0.rst │ │ │ ├── gatk4_germlinevariantcaller_4.1.3.0.rst │ │ │ ├── gatk4_somaticvariantcaller.rst │ │ │ ├── gatk4_somaticvariantcaller_4.0.12.0.rst │ │ │ ├── gatk4_somaticvariantcaller_4.1.3.0.rst │ │ │ ├── gatk4_somaticvariantcallertumoronlytargeted.rst │ │ │ ├── gatk4_somaticvariantcallertumoronlytargeted_v0.1.1.rst │ │ │ ├── index.rst │ │ │ ├── strelkaGermlineVariantCaller_v0_1_1.dot │ │ │ ├── strelkaGermlineVariantCaller_v0_1_1.dot.png │ │ │ ├── strelkaSomaticVariantCaller_v0_1_1.dot │ │ │ ├── strelkaSomaticVariantCaller_v0_1_1.dot.png │ │ │ ├── strelkagermlinevariantcaller.rst │ │ │ ├── strelkagermlinevariantcaller_v0.1.1.rst │ │ │ ├── strelkasomaticvariantcaller.rst │ │ │ ├── strelkasomaticvariantcaller_v0.1.1.rst │ │ │ ├── vardictGermlineVariantCaller_v0_1_1.dot │ │ │ ├── vardictGermlineVariantCaller_v0_1_1.dot.png │ │ │ ├── vardictSomaticVariantCaller_v0_1_0.dot │ │ │ ├── vardictSomaticVariantCaller_v0_1_0.dot.png │ │ │ ├── vardictgermlinevariantcaller.rst │ │ │ ├── vardictgermlinevariantcaller_v0.1.1.rst │ │ │ ├── vardictsomaticvariantcaller.rst │ │ │ └── vardictsomaticvariantcaller_v0.1.0.rst │ │ ├── vcftools │ │ │ ├── index.rst │ │ │ ├── vcftools.rst │ │ │ ├── vcftools_0.1.16.rst │ │ │ ├── vcftoolsvcfconcat.rst │ │ │ ├── vcftoolsvcfconcat_0.1.16.rst │ │ │ ├── vcftoolsvcfmerge.rst │ │ │ └── vcftoolsvcfmerge_0.1.16.rst │ │ └── whisper │ │ │ ├── index.rst │ │ │ ├── whisperalign.rst │ │ │ ├── whisperalign_v2.0.rst │ │ │ ├── whisperindex.rst │ │ │ └── whisperindex_v2.0.rst │ ├── index.rst │ └── unix │ │ ├── awk.rst │ │ ├── awk_v1.0.0.rst │ │ ├── cat.rst │ │ ├── cat_v1.0.0.rst │ │ ├── echo.rst │ │ ├── echo_v1.0.0.rst │ │ ├── hello.rst │ │ ├── hello_v1.0.0.rst │ │ ├── hello_v1_0_0.dot │ │ ├── hello_v1_0_0.dot.png │ │ ├── index.rst │ │ ├── javacompiler.rst │ │ ├── javacompiler_v1.0.0.rst │ │ ├── md5sum.rst │ │ ├── md5sum_v1.0.0.rst │ │ ├── sleep.rst │ │ ├── sleep_v1.0.0.rst │ │ ├── tar.rst │ │ ├── tar_v1.0.0.rst │ │ ├── uncompressarchive.rst │ │ ├── uncompressarchive_v1.0.0.rst │ │ ├── untar.rst │ │ └── untar_v1.0.0.rst ├── tutorials │ ├── collectingoutputs.rst │ ├── container.md │ ├── hpcconfiguration.md │ ├── running.md │ ├── toolbox.md │ ├── tutorial0.md │ ├── tutorial1.md │ ├── tutorial2.md │ └── tutorial3.md └── userguide.rst ├── examples ├── README.md ├── __init__.py ├── dynamicworkflow.py ├── echo.py ├── secondaryfiles.py ├── simple.md ├── simple.py └── simplewrapped.py ├── janis ├── __init__.py ├── __meta__.py ├── data_types │ └── __init__.py └── tools │ └── __init__.py ├── janisdk ├── __init__.py ├── container │ ├── __init__.py │ ├── parse_help.py │ └── test_cltbuilder.py ├── fromcwl │ └── __init__.py ├── fromwdl │ └── __init__.py ├── main.py └── runtest │ ├── __init__.py │ └── runner.py ├── notebooks ├── simple.png └── workshop1.ipynb ├── presentations └── 2019-12-10 - ABACBS.pptx ├── progress └── 2019-02.md ├── pyproject.toml ├── setup.py └── updatesubmodules.sh /.github/workflows/publish.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PMCC-BioinformaticsCore/janis/HEAD/.github/workflows/publish.yml -------------------------------------------------------------------------------- /.github/workflows/unit_tests.yml: -------------------------------------------------------------------------------- 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