Explore Workflows
View already parsed workflows here or click here to add your own
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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 |
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tt_kmer_compare_wnode
Pairwise comparison |
https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_compare_wnode.cwl Branch/Commit ID: 609aead9804a8f31fa9b3dbc7e52105aec487f31 |
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wf_demultiplex_se.cwl
This workflow takes in single-end reads, and performs the following steps in order: demux_se.cwl (does not actually demux for single end, but mirrors the paired-end processing protocol) |
https://github.com/YeoLab/eclip.git
Path: cwl/wf_demultiplex_se.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/22-nested-workflows/1st-workflow.cwl Branch/Commit ID: 4ecdd01e38fc9572248e514907171bb9fde5063a |
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trimmed_fastq
Quality Control and Raw Data trimming |
https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/subworkflows/trimmed_fastq.cwl Branch/Commit ID: d07f44fc5c253dc4044d86ea79ac6f9e03c01bfa |
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cnv_exomedepth
CNV ExomeDepth calling |
https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/subworkflows/cnv_exome_depth.cwl Branch/Commit ID: d07f44fc5c253dc4044d86ea79ac6f9e03c01bfa |
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Seed Search Compartments
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https://github.com/ncbi/pgap.git
Path: protein_alignment/wf_seed.cwl Branch/Commit ID: 9362082213e20315f76f6f5c235cac3aae565747 |
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wf_trim_partial_and_map_se_scatter.cwl
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https://github.com/YeoLab/eclip.git
Path: cwl/wf_trim_partial_and_map_se_scatter.cwl Branch/Commit ID: 49a9bcda10de8f55fab2481f424eb9cdf2e5b256 |
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Single-cell Differential Expression
Single-cell Differential Expression =================================== Runs differential expression analysis for a subset of cells between two selected conditions. |
https://github.com/datirium/workflows.git
Path: workflows/sc_diff_expr.cwl Branch/Commit ID: e45ab1b9ac5c9b99fdf7b3b1be396dc42c2c9620 |
