├── .gitignore ├── README.md ├── cwl2wdl ├── __init__.py ├── base_classes.py ├── generators.py ├── main.py └── parsers.py ├── cwl2wdl_dev.py ├── requirements.txt ├── setup.cfg ├── setup.py └── tests └── cwl ├── README.md ├── tools ├── GATK-BaseRecalibrator.cwl ├── GATK-FastaAlternateReferenceMaker.cwl ├── GATK-HaplotypeCaller.cwl ├── GATK-IndelRealigner.cwl ├── GATK-PrintReads.cwl ├── GATK-RealignTargetCreator.cwl ├── GATK-docker.cwl ├── STAR.cwl ├── alea-alignReads.cwl ├── alea-createGenome.cwl ├── alea-docker.cwl ├── alea-insilico.cwl ├── alea-phaseVCF.cwl ├── bcftools-concat.cwl ├── bcftools-consensus.cwl ├── bcftools-docker.cwl ├── bedtools-docker.cwl ├── bedtools-genomecov-types.cwl ├── bedtools-genomecov.cwl ├── bowtie.cwl ├── bwa-docker.cwl ├── envvar-global.cwl ├── linux-sort-docker.cwl ├── linux-sort.cwl ├── node-engine.cwl ├── picard-BuildBamIndex.cwl ├── picard-CreateSequenceDictionary.cwl ├── picard-MarkDuplicates.cwl ├── picard-MergeSamFiles.cwl ├── picard-SortSam.cwl ├── picard-docker.cwl ├── samtools-docker.cwl ├── samtools-faidx.cwl ├── samtools-index.cwl ├── samtools-rmdup.cwl ├── samtools-sort.cwl ├── samtools-view.cwl ├── ucsc-bedGraphToBigWig.cwl ├── ucsc-liftOver.cwl └── ucsc-userapps-docker.cwl └── workflows ├── FestivalDemo ├── README ├── filtercount-job.json ├── filtercount.cwl.yaml ├── grep.cwl.yaml ├── mock.txt ├── mock2.txt └── wc.cwl.yaml ├── compile ├── README.md ├── compile1.cwl ├── source1.c ├── source1.h └── source2.c ├── hello ├── README.md ├── hello-param.cwl ├── hello.cwl └── params.json ├── lobSTR ├── README ├── allelotype.cwl ├── lobSTR-arvados-demo.json ├── lobSTR-demo.json ├── lobSTR-tool.cwl ├── lobSTR-workflow.cwl ├── models │ ├── illumina_v3.pcrfree.stepmodel │ └── illumina_v3.pcrfree.stuttermodel ├── node-engine.cwl ├── samtools-index.cwl ├── samtools-sort.cwl ├── tmp_1.fq └── tmp_2.fq ├── make-to-cwl ├── Makefile ├── README.md ├── dna.cwl └── rna.json └── scidap ├── bam-genomecov-bigwig-job.json ├── 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