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Graph Name Retrieved From View
workflow graph facets-workflow.cwl

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: master
workflow graph main-somatic.cwl

https://github.com/farahzkhan/bcbio_test_cwlprov.git

Path: somatic/somatic-workflow/main-somatic.cwl

Branch/Commit ID: master
workflow graph kallisto-demo.cwl

https://github.com/common-workflow-library/legacy.git

Path: workflows/kallisto-demo.cwl

Branch/Commit ID: master
workflow graph RMSynth Workflow

https://github.com/as595/cwl_rmsynth.git

Path: rmsynth_workflow1.cwl

Branch/Commit ID: master
workflow graph pangenome-generate_spoa.cwl

https://github.com/arvados/czi-pangenome-usecase.git

Path: pangenome-generate_spoa.cwl

Branch/Commit ID: main
workflow graph black-diamond-workflow.cwl

https://github.com/ryantanaka/cwl-vs-dax-example.git

Path: black-diamond-workflow/cwl/black-diamond-workflow.cwl

Branch/Commit ID: master
workflow graph diffbind-parallel.cwl

https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/ChIP-Seq/diffbind-parallel.cwl

Branch/Commit ID: master
workflow graph dedup-2-pass-distr.cwl

run 2-pass dedup: algo LocusCollector + algo Dedup sequentially in distributed mode

 https://github.com/Sentieon/Sentieon-cwl.git

Path: stage/dedup-2-pass-distr.cwl

Branch/Commit ID: master
workflow graph protein annotation

Proteins - predict, cluster, identify, annotate

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/protein-annotation.workflow.cwl

Branch/Commit ID: master
workflow graph sc_atac_seq_process_and_analyze.cwl

https://github.com/hubmapconsortium/sc-atac-seq-pipeline.git

Path: steps/sc_atac_seq_process_and_analyze.cwl

Branch/Commit ID: d0e845d