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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: 7eb2b0a4d37018142233d770595ac2e00376dab4

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

Path: tests/wf/scatter-wf4.cwl

Branch/Commit ID: 7dec97bb8f0bc2d9e9eb710faf41f2e98cc7cdda

Packed ID: main

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: e3f18c61d1bbf65e40921dbd044369da4523ee3e

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_create_readme/readme-assembly-workflow.cwl

Branch/Commit ID: 89cff9f0d36a23bf57b3f4bdbd3ed57e3347c945

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

Path: definitions/subworkflows/varscan_germline.cwl

Branch/Commit ID: a08de598edc04f340fdbff76c9a92336a7702022

Workflow to run GetBaseCountsMultiSample fillout on a number of samples, each with their own bam and maf files

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

Path: cwl/samples_fillout_workflow.cwl

Branch/Commit ID: 7eb2b0a4d37018142233d770595ac2e00376dab4

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

Path: task_types/tt_kmer_top_n.cwl

Branch/Commit ID: 369afa7090a7480e6a0b144eff967a4a52b6fde2

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

Path: task_types/tt_cache_asnb_entries.cwl

Branch/Commit ID: d39017c63dd8e088f1ad3809d709529df602e05f

Devel version of Single-Cell Preprocessing Cell Ranger Pipeline ===============================================================

https://github.com/datirium/workflows.git

Path: workflows/single-cell-preprocess-cellranger.cwl

Branch/Commit ID: 7fb8a1ebf8145791440bc2fed9c5f2d78a19d04c

Generates ATDP heatmap centered on TSS from an array of input BAM files and genelist TSV file. Returns array of heatmap JSON files with the names that have the same basenames as input BAM files, but with .json extension

https://github.com/Barski-lab/workflows.git

Path: workflows/heatmap.cwl

Branch/Commit ID: bc75349ad3a7bdce82b4cd8584501f4d0280bb8d