Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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Pairwise genomic regions intersection
Pairwise genomic regions intersection ============================================= Overlaps peaks from two ChIP/ATAC experiments |
https://github.com/datirium/workflows.git
Path: workflows/peak-intersect.cwl Branch/Commit ID: c6bfa0de917efb536dd385624fc7702e6748e61d |
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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: c64599f5db2437f9323d41cc3d8d9efb20a2667e |
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bacterial_orthology
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https://github.com/ncbi/pgap.git
Path: bacterial_orthology/wf_bacterial_orthology.cwl Branch/Commit ID: c64599f5db2437f9323d41cc3d8d9efb20a2667e |
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Seed Protein Alignments
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https://github.com/ncbi/pgap.git
Path: protein_alignment/wf_seed_seqids.cwl Branch/Commit ID: c64599f5db2437f9323d41cc3d8d9efb20a2667e |
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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: 69643d8c15f5357a320aa7e2f6adb2e71302fd20 |
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blastp_wnode_struct
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https://github.com/ncbi/pgap.git
Path: task_types/tt_blastp_wnode_struct.cwl Branch/Commit ID: c64599f5db2437f9323d41cc3d8d9efb20a2667e |
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blastp_wnode_naming
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https://github.com/ncbi/pgap.git
Path: task_types/tt_blastp_wnode_naming.cwl Branch/Commit ID: c64599f5db2437f9323d41cc3d8d9efb20a2667e |
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trnascan_wnode and gpx_qdump combined
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https://github.com/ncbi/pgap.git
Path: bacterial_trna/wf_scan_and_dump.cwl Branch/Commit ID: c64599f5db2437f9323d41cc3d8d9efb20a2667e |
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exome alignment and germline variant detection
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/germline_exome.cwl Branch/Commit ID: 22fce2dbdada0c4135b6f0677f78535cf980cb07 |
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chipseq-gen-bigwig.cwl
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https://github.com/Barski-lab/workflows.git
Path: workflows/chipseq-gen-bigwig.cwl Branch/Commit ID: ca2dbb71d0537b1d93a8bd44719250cf8949b157 |
