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: b957a4f681bf0ca8ebba4e0d0ec3936bf79620c5
workflow graph count-lines10-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines10-wf.cwl

Branch/Commit ID: d7cd45f7072960d264962ecc5a04d7c219f65c06
workflow graph count-lines6-wf.cwl

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

Path: v1.0/v1.0/count-lines6-wf.cwl

Branch/Commit ID: 148f11b11d31c098196e649f680797f0b4680114
workflow graph scatter-wf1.cwl

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

Path: cwltool/schemas/v1.0/v1.0/scatter-wf1.cwl

Branch/Commit ID: 814bd0405a7701efc7d63e8f0179df394c7766f7
workflow graph count-lines11-extra-step-wf.cwl

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

Path: v1.0/v1.0/count-lines11-extra-step-wf.cwl

Branch/Commit ID: 40fcfc01812046f012acf5153cc955ee848e69e3
workflow graph count-lines7-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines7-wf.cwl

Branch/Commit ID: e8b3565a008d95859fc44227987a54e6a53a8c29
workflow graph count-lines18-wf.cwl

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

Path: v1.0/v1.0/count-lines18-wf.cwl

Branch/Commit ID: 40fcfc01812046f012acf5153cc955ee848e69e3
workflow graph schemadef-wf.cwl

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

Path: v1.0/v1.0/schemadef-wf.cwl

Branch/Commit ID: fe164457f370c2dfec5156f6d6d45818d53cb871
workflow graph schemadef-wf.cwl

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

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

Branch/Commit ID: 520acbfb82455c4bdabd5f2ea24842804e1c9f58
workflow graph step-valuefrom5-wf.cwl

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

Path: v1.0/v1.0/step-valuefrom5-wf.cwl

Branch/Commit ID: 148f11b11d31c098196e649f680797f0b4680114