Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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05-quantification.cwl
ChIP-seq - Quantification - samples: treatment |
https://github.com/Duke-GCB/GGR-cwl.git
Path: v1.0/ChIP-seq_pipeline/05-quantification.cwl Branch/Commit ID: master |
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readme-genePrediction-workflow.cwl
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https://github.com/NAL-i5K/Organism_Onboarding.git
Path: flow_create_readme/readme-genePrediction-workflow.cwl Branch/Commit ID: master |
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readme-assembly-workflow.cwl
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https://github.com/NAL-i5K/Organism_Onboarding.git
Path: flow_create_readme/readme-assembly-workflow.cwl Branch/Commit ID: master |
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fastqPE2bam.cwl
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https://github.com/ddbj/human-reseq.git
Path: Workflows/fastqPE2bam.cwl Branch/Commit ID: master |
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snapanalysis_setup_and_analyze.cwl
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https://github.com/hubmapconsortium/sc-atac-seq-pipeline.git
Path: steps/snapanalysis_setup_and_analyze.cwl Branch/Commit ID: 5465f66 |
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echo-wc.cwl
Counts words of a message via echo and wc |
https://github.com/NLeSC/scriptcwl.git
Path: tests/data/workflows/echo-wc.cwl Branch/Commit ID: master |
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extract_gencoll_ids
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https://github.com/ncbi/pgap.git
Path: task_types/tt_extract_gencoll_ids.cwl Branch/Commit ID: test |
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Functional analyis of sequences that match the 16S SSU
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https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git
Path: workflows/16S_taxonomic_analysis.cwl Branch/Commit ID: 135976d |
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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: master |
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CRAM_md5sum.cwl
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https://github.com/DataBiosphere/topmed-workflows.git
Path: CRAM-no-header-md5sum/md5sum/CRAM_md5sum.cwl Branch/Commit ID: 1.23.0 |
