Explore Workflows
View already parsed workflows here or click here to add your own
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Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/pvacseq.cwl Branch/Commit ID: 9161ef43f7bf0e22b365fde9ec92edcb8601798e |
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exome alignment and germline variant detection
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/germline_detect_variants.cwl Branch/Commit ID: 9e5f228bc1a3d0dfe950b5d41d7e4319e834a6d4 |
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bam-bedgraph-bigwig.cwl
Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow. |
https://github.com/datirium/workflows.git
Path: tools/bam-bedgraph-bigwig.cwl Branch/Commit ID: 8bf36bfad5624fbc8fc315e82783a44e9e5e4470 |
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Bisulfite QC tools
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/bisulfite_qc.cwl Branch/Commit ID: 9161ef43f7bf0e22b365fde9ec92edcb8601798e |
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bacterial_kmer
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https://github.com/ncbi/pgap.git
Path: bacterial_kmer/wf_bacterial_kmer.cwl Branch/Commit ID: 4f4448f71645275db5b84eb551990dfe3bf37cbb |
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download_root.cwl
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https://github.com/nci-gdc/gdc-dnaseq-cwl.git
Path: workflows/unix/download_root.cwl Branch/Commit ID: 1046947f8d2923e6563b3aceac9e435554c5bea1 |
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Run genomic CMsearch
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https://github.com/ncbi/pgap.git
Path: bacterial_noncoding/wf_gcmsearch.cwl Branch/Commit ID: 7c8eb4d23c3c9859f57421643710c0b6d57b606c |
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Bacterial Annotation, pass 3, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)
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https://github.com/ncbi/pgap.git
Path: bacterial_annot/wf_bacterial_annot_pass3.cwl Branch/Commit ID: 7c8eb4d23c3c9859f57421643710c0b6d57b606c |
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status_postgres_workflow.cwl
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https://github.com/NCI-GDC/gdc-dnaseq-cwl.git
Path: workflows/status/status_postgres_workflow.cwl Branch/Commit ID: 23819c2a0dcd98b61487cbc82e602dd58cb4d342 |
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spurious_annot
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https://github.com/ncbi/pgap.git
Path: spurious_annot/wf_spurious_annot_pass1.cwl Branch/Commit ID: 7c8eb4d23c3c9859f57421643710c0b6d57b606c |
