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Workflow for running Facets-suite on a set of tumor normal pairs This workflow scatters over all the pairs in the input JSON to run all samples in parallel Input JSON format ----------------- { \"pairs\": [ { \"tumor_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor1.rg.md.abra.printreads.bam\" }, \"normal_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Normal1.rg.md.abra.printreads.bam\" }, \"pair_maf\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor1.Normal1.maf\" }, \"pair_id\": \"Tumor1.Normal1\" }, { \"tumor_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor2.rg.md.abra.printreads.bam\" }, \"normal_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Normal2.rg.md.abra.printreads.bam\" }, \"pair_maf\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor2.Normal2.maf\" }, \"pair_id\": \"Tumor2.Normal2\" } ] } Output format ------------- output └── facets-suite ├── Tumor1.Normal1.arm_level.txt ├── Tumor1.Normal1.gene_level.txt ├── Tumor1.Normal1_hisens.ccf.maf ├── Tumor1.Normal1_hisens.rds ├── Tumor1.Normal1_hisens.seg ├── Tumor1.Normal1_purity.rds ├── Tumor1.Normal1_purity.seg ├── Tumor1.Normal1.qc.txt ├── Tumor1.Normal1.snp_pileup.gz ├── Tumor1.Normal1.txt ├── Tumor2.Normal2.arm_level.txt ├── Tumor2.Normal2.gene_level.txt ├── Tumor2.Normal2_hisens.ccf.maf ├── Tumor2.Normal2_hisens.rds ├── Tumor2.Normal2_hisens.seg ├── Tumor2.Normal2_purity.rds ├── Tumor2.Normal2_purity.seg ├── Tumor2.Normal2.qc.txt ├── Tumor2.Normal2.snp_pileup.gz ├── Tumor2.Normal2.txt └── logs ├── success └── failed

https://github.com/mskcc/pluto-cwl.git

Path: cwl/facets-workflow.cwl

Branch/Commit ID: c10d8bcf045067b3510bff68e2e957fccea0d7ea

https://github.com/ncbi/pgap.git

Path: task_types/tt_cluster_and_qdump.cwl

Branch/Commit ID: 3472e6539f6abbc3aa77db22d5816b9e96647f5e

https://github.com/common-workflow-language/cwl-utils.git

Path: testdata/cond-wf-003.1.cwl

Branch/Commit ID: e413f9b185f0060ffbdd876062133d65daecb7da

https://github.com/kids-first/kf-rnaseq-workflow.git

Path: workflow/personal_genome_input_wf.cwl

Branch/Commit ID: 23efbed9d7faa40e6d6e8d85441887a003fafda5

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/iwdr_with_nested_dirs.cwl

Branch/Commit ID: 5e3fac092a720c5670ae3e787eabe1aaade71d83

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/pindel_region.cwl

Branch/Commit ID: 046e980d131ebaf71f76599a749e2294c40c9d0d

https://github.com/ncbi/pgap.git

Path: task_types/tt_fscr_calls_pass1.cwl

Branch/Commit ID: 192b813eed8c0d368e69057cb39415175dd15128

https://github.com/inab/Wetlab2Variations.git

Path: cwl-workflows/demonstrator/workflow_localfiles.cwl

Branch/Commit ID: 5e109429c3b59a8e79cc18f614c4218dbc4fc9ea

https://github.com/ebi-jdispatcher/webservice-cwl.git

Path: workflows/workflow-pepinfo-backtranseq-cpgplot.cwl

Branch/Commit ID: 88b9948c4977ca90ab5ceb391b2235043135480d

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/count-lines6-wf.cwl

Branch/Commit ID: 17268d1493d9e558113b2c35c0be6b3fb961b2a3