Explore Workflows
View already parsed workflows here or click here to add your own
Graph | Name | Retrieved From | View |
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bulk scRNA-seq pipeline using Salmon
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https://github.com/hubmapconsortium/salmon-rnaseq.git
Path: bulk-pipeline.cwl Branch/Commit ID: 9af9cb1f5e65c2d10e0f1611a9a2f913ef206928 |
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workflow.cwl
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https://github.com/NAL-i5K/Organism_Onboarding.git
Path: flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl Branch/Commit ID: 89cff9f0d36a23bf57b3f4bdbd3ed57e3347c945 |
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workflow-ebisearch.cwl
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https://github.com/ebi-wp/webservice-cwl.git
Path: workflows/workflow-ebisearch.cwl Branch/Commit ID: 5df6b762980b15b0f6389149311b82bdd6dff37d |
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wf_trim_and_map_pe.cwl
This workflow takes in appropriate trimming params and demultiplexed reads, and performs the following steps in order: trimx1, trimx2, fastq-sort, filter repeat elements, fastq-sort, genomic mapping, sort alignment, index alignment, namesort, PCR dedup, sort alignment, index alignment |
https://github.com/YeoLab/eclip.git
Path: cwl/wf_trim_and_map_pe.cwl Branch/Commit ID: 49a9bcda10de8f55fab2481f424eb9cdf2e5b256 |
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Single-Cell Preprocessing Pipeline
Devel version of Single-Cell Preprocessing Pipeline =================================================== |
https://github.com/datirium/workflows.git
Path: workflows/single-cell-preprocess.cwl Branch/Commit ID: e45ab1b9ac5c9b99fdf7b3b1be396dc42c2c9620 |
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bwa_mem
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https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/subworkflows/bwa_mem.cwl Branch/Commit ID: d07f44fc5c253dc4044d86ea79ac6f9e03c01bfa |
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concat.cwl
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https://github.com/mskcc/pluto-cwl.git
Path: cwl/concat.cwl Branch/Commit ID: d8a8af9fdb69c0a4003680c1d3b96f35d5e48f0e |
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wf_demultiplex_pe.cwl
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https://github.com/YeoLab/eclip.git
Path: cwl/wf_demultiplex_pe.cwl Branch/Commit ID: 49a9bcda10de8f55fab2481f424eb9cdf2e5b256 |
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1st-workflow.cwl
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https://github.com/common-workflow-language/user_guide.git
Path: _includes/cwl/21-1st-workflow/1st-workflow.cwl Branch/Commit ID: 4ecdd01e38fc9572248e514907171bb9fde5063a |
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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: d8a8af9fdb69c0a4003680c1d3b96f35d5e48f0e |