Explore Workflows

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: bf80c9339d81a78aefb8de661bff998ed86e836e

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

Path: cwltool/schemas/v1.0/v1.0/count-lines9-wf.cwl

Branch/Commit ID: fd6e054510e2bb65eed4069a3a88013d7ecbb99c

https://github.com/andurill/ACCESS-Pipeline.git

Path: workflows/waltz/waltz_workflow_all_bams.cwl

Branch/Commit ID: f8b57834ad0ce78e4d5bdd90ed0991923685d87f

https://github.com/proteinswebteam/ebi-metagenomics-cwl.git

Path: tools/SSU-from-tablehits.cwl

Branch/Commit ID: 708fd971bd3abe4d367e501583b964bc4c0311b9

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

Path: definitions/subworkflows/align.cwl

Branch/Commit ID: 31a179d7a2f2ac86bfd7fcc4dc79832c3739ae76

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

Path: definitions/subworkflows/varscan_germline.cwl

Branch/Commit ID: d57c2af01a3cb6016e5a264f60641eafd2e5aa05

Reverse the lines in a document, then sort those lines.

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

Path: tests/wf/revsort.cwl

Branch/Commit ID: 6003cbb94f16103241b562f2133e7c4acac6c621

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

Path: cwltool/schemas/v1.0/v1.0/conflict-wf.cwl

Branch/Commit ID: fc6ca8b1498926f705dcfde7ab0a365bd09a9675

Packed ID: collision

This workflow will run OxoG, variantbam, and annotate. Run this as `dockstore --script --debug workflow launch --descriptor cwl --local-entry --entry ./oxog_varbam_annotate_wf.cwl --json oxog_varbam_annotat_wf.input.json `

https://github.com/svonworl/OxoG-Dockstore-Tools.git

Path: oxog_varbam_annotate_wf.cwl

Branch/Commit ID: 40bf56daf9edab82e0f964dbd6961ca1111cd35f

https://github.com/alexandersenf/orgaquant.git

Path: orgaquant_wf.cwl

Branch/Commit ID: 2bf644451019b6a483a84c730075e7038bc6868c