Explore Workflows
View already parsed workflows here or click here to add your own
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taxcheck.cwl
Perform taxonomic identification tasks on an input genome |
https://github.com/ncbi/pgap.git
Path: taxcheck.cwl Branch/Commit ID: 4e7b8f243f5356653edd286eab24f419f39da189 |
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kmer_build_tree
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_build_tree.cwl Branch/Commit ID: 4e7b8f243f5356653edd286eab24f419f39da189 |
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protein_extract
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https://github.com/ncbi/pgap.git
Path: progs/protein_extract.cwl Branch/Commit ID: 4e7b8f243f5356653edd286eab24f419f39da189 |
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kmer_cache_store
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_cache_store.cwl Branch/Commit ID: 4e7b8f243f5356653edd286eab24f419f39da189 |
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CGC-subwf.cwl
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https://github.com/EBI-Metagenomics/pipeline-v5.git
Path: workflows/subworkflows/assembly/CGC-subwf.cwl Branch/Commit ID: 49ae257c560e71d2946290d1705b2912fd81f76f |
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func_ann_and_post_processing-subwf.cwl
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https://github.com/EBI-Metagenomics/pipeline-v5.git
Path: workflows/subworkflows/assembly/func_ann_and_post_processing-subwf.cwl Branch/Commit ID: 49ae257c560e71d2946290d1705b2912fd81f76f |
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final_chunking.cwl
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https://github.com/EBI-Metagenomics/pipeline-v5.git
Path: workflows/subworkflows/final_chunking.cwl Branch/Commit ID: 49ae257c560e71d2946290d1705b2912fd81f76f |
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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: 3bc4fab5503e58521ed0eb9c0d035ac18460dc13 |
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spurious_annot pass2
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https://github.com/ncbi/pgap.git
Path: spurious_annot/wf_spurious_annot_pass2.cwl Branch/Commit ID: 4e7b8f243f5356653edd286eab24f419f39da189 |
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scatter-wf3.cwl#main
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https://github.com/common-workflow-language/cwl-v1.2.git
Path: tests/scatter-wf3.cwl Branch/Commit ID: 4fa45edd0c445c1cff7dee986d69a31cdd5e5dff Packed ID: main |
