Explore Workflows
View already parsed workflows here or click here to add your own
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canine_add_matched_rna.cwl
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https://github.com/d3b-center/canine-dev.git
Path: subworkflows/canine_add_matched_rna.cwl Branch/Commit ID: 462aaebbd442e84ea101b45b716df0174b88512e |
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Run genomic CMsearch (Rfam rRNA)
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https://github.com/ncbi/pgap.git
Path: bacterial_ncrna/wf_gcmsearch.cwl Branch/Commit ID: 8c21035bff3cbffccf5682bd0357a6d71f3bdb81 |
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FASTQ Vector Removal
This workflow clean up vectros from fastq files |
https://github.com/ncbi/cwl-ngs-workflows-cbb.git
Path: workflows/Contamination/fastq-vector-removal.cwl Branch/Commit ID: b5a440939ac6022ee81aeeb0dd7daf3983228a61 |
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sample-workflow.cwl
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https://github.com/mskcc/argos-cwl.git
Path: workflows/sample-workflow.cwl Branch/Commit ID: eb1c641d3134e7e13bc1a15fe7d8de7937527aca |
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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: dbff0c5ae06a8b21ec70bc8279f32bce151cbfc2 |
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fastq_foreign_chromosome_cleanup
This workflow remove foreign chromosome comtamination from blastn TSV files |
https://github.com/ncbi/cwl-ngs-workflows-cbb.git
Path: workflows/Contamination/fastq-foreign-chromosome-cleanup.cwl Branch/Commit ID: b5a440939ac6022ee81aeeb0dd7daf3983228a61 |
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stdout-wf_v1_0.cwl
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https://github.com/common-workflow-language/cwl-utils.git
Path: testdata/stdout-wf_v1_0.cwl Branch/Commit ID: 139c64b55f7693d22e6646b8afe585f90da11dcb |
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scatter GATK HaplotypeCaller over intervals
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/gatk_haplotypecaller_iterator.cwl Branch/Commit ID: 60d8a9e6c5f571ec9b37f10290a1f4613013f3e1 |
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scatter-wf2_v1_0.cwl
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https://github.com/common-workflow-language/cwl-utils.git
Path: testdata/scatter-wf2_v1_0.cwl Branch/Commit ID: c46a3ad4e488e75b7a58032c129f0605f5e84f40 |
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Apply filters to VCF file
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/filter_vcf.cwl Branch/Commit ID: 0c4f4e59c265eb22aed3d2d37b173cb5430773d2 |
