Explore Workflows

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Graph Name Retrieved From View
workflow graph 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
workflow graph blastp_wnode_struct

https://github.com/ncbi/pgap.git

Path: task_types/tt_blastp_wnode_struct.cwl

Branch/Commit ID: c64599f5db2437f9323d41cc3d8d9efb20a2667e
workflow graph blastp_wnode_naming

https://github.com/ncbi/pgap.git

Path: task_types/tt_blastp_wnode_naming.cwl

Branch/Commit ID: c64599f5db2437f9323d41cc3d8d9efb20a2667e
workflow graph trnascan_wnode and gpx_qdump combined

https://github.com/ncbi/pgap.git

Path: bacterial_trna/wf_scan_and_dump.cwl

Branch/Commit ID: c64599f5db2437f9323d41cc3d8d9efb20a2667e
workflow graph exome alignment and germline variant detection

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/germline_exome.cwl

Branch/Commit ID: 22fce2dbdada0c4135b6f0677f78535cf980cb07
workflow graph chipseq-gen-bigwig.cwl

https://github.com/Barski-lab/workflows.git

Path: workflows/chipseq-gen-bigwig.cwl

Branch/Commit ID: ca2dbb71d0537b1d93a8bd44719250cf8949b157
workflow graph directory.cwl

Inspect provided directory and return filenames. Generate a new directory and return it (including content).

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/directory.cwl

Branch/Commit ID: 83038feb2a6fc3bab952e1ecc2a11bfbc8c557b4
workflow graph basename-fields-test.cwl

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/basename-fields-test.cwl

Branch/Commit ID: 65aedc5e7e1f3ccace7f9022f8a54b3f0d5c9a8c
workflow graph scatter-valuefrom-wf3.cwl#main

https://github.com/common-workflow-language/common-workflow-language.git

Path: v1.0/v1.0/scatter-valuefrom-wf3.cwl

Branch/Commit ID: 4fd45edb9531a03223c18a586e32d0baf0d5acb2

Packed ID: main
workflow graph group-isoforms-batch.cwl

Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored.

https://github.com/datirium/workflows.git

Path: tools/group-isoforms-batch.cwl

Branch/Commit ID: c6bfa0de917efb536dd385624fc7702e6748e61d