Explore Workflows
View already parsed workflows here or click here to add your own
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Bacterial Annotation, pass 3, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)
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https://github.com/ncbi/pgap.git
Path: bacterial_annot/wf_bacterial_annot_pass3.cwl Branch/Commit ID: 6a29751f2b16659c1592f1e94837c989e68f3b8b |
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count-lines3-wf.cwl
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https://github.com/common-workflow-language/cwl-v1.1.git
Path: tests/count-lines3-wf.cwl Branch/Commit ID: 5e3fac092a720c5670ae3e787eabe1aaade71d83 |
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HBA_calibrator.cwl
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https://git.astron.nl/eosc/prefactor3-cwl.git
Path: workflows/HBA_calibrator.cwl Branch/Commit ID: b6fabaa851824677da26f8240e27e832b98f666d |
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gathered exome alignment and somatic variant detection
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/somatic_exome_gathered.cwl Branch/Commit ID: 2e298960837739717ec2928a99c5d811183012e6 |
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lhcbreconstruct.cwl
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https://github.com/aldbr/dirac-cwl-proto.git
Path: test/workflows/lhcb/lhcbreconstruct.cwl Branch/Commit ID: 0a7ab0154feadd641e17fdcabf3f0b83105fd4df |
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three_step_color.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/three_step_color.cwl Branch/Commit ID: f6aeeae01ca1d821f2be1966f48f5257100f90e5 |
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RNA-Seq alignment and transcript/gene abundance workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/rnaseq.cwl Branch/Commit ID: d57c2af01a3cb6016e5a264f60641eafd2e5aa05 |
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Tumor-Only Detect Variants workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/tumor_only_detect_variants.cwl Branch/Commit ID: 26806d99f8e2a241715fd081e712d4e3763db5b8 |
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wgs alignment with qc
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/wgs_alignment.cwl Branch/Commit ID: 26806d99f8e2a241715fd081e712d4e3763db5b8 |
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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: c10d8bcf045067b3510bff68e2e957fccea0d7ea |
