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: cc6fa135d04737fdde3b4414d6e214cf8c812f6e
workflow graph record-output-wf.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/record-output-wf.cwl

Branch/Commit ID: b1d4a69df86350059bd49aa127c02be0c349f7de
workflow graph step-valuefrom-wf.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/step-valuefrom-wf.cwl

Branch/Commit ID: b1d4a69df86350059bd49aa127c02be0c349f7de
workflow graph count-lines18-wf.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/count-lines18-wf.cwl

Branch/Commit ID: 368b562a1449e8cd39ae8b7f05926b2bfb9b22df
workflow graph composed_workflows.cwl

https://github.com/giannisdoukas/CWLJNIKernel.git

Path: tests/cwl/composed_workflows.cwl

Branch/Commit ID: e07959c147a9a4f5470f5ed3c22e37356ec92197
workflow graph Uses Bruker TopSpin to convert a zipped NMR data directory to JCAMP-DX

https://github.com/NFDI4Chem/formaTAPIRest.git

Path: cwl/zipped2bruker2jcamp.cwl

Branch/Commit ID: da8a0496d4fbe1815dc978a5ceaa183b7cb73cf1
workflow graph rnaseq-alignment-quantification

This workflow retrieve SRA fastqc data and execute QC, alignment and quantification from TPMCalculator

 https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/RNA-Seq/rnaseq-quantification-qc.cwl

Branch/Commit ID: 1b1cb5bbbe53a2dd5d7de7cdbff19c1bdbe23a49
workflow graph call_variants.cwl

https://github.com/mskcc/Innovation-Pipeline.git

Path: workflows/subworkflows/call_variants.cwl

Branch/Commit ID: b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf
workflow graph vcf.gz2bed.cwl

https://github.com/biosciencedbc/jga-analysis.git

Path: multi-samples/Workflows/vcf.gz2bed.cwl

Branch/Commit ID: main
workflow graph no-inputs-wf.cwl

Workflow without inputs.

 https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/no-inputs-wf.cwl

Branch/Commit ID: b1d4a69df86350059bd49aa127c02be0c349f7de