Explore Workflows

View already parsed workflows here or click here to add your own

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: 1131f82a53315cca217a6c84b3bd272aa62e4bca
workflow graph nestedworkflows.cwl

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

Path: _includes/cwl/22-nested-workflows/nestedworkflows.cwl

Branch/Commit ID: 4af7d2c63a1604b4558bd616ccd7dbb664fd8d1b
workflow graph blastp_wnode_naming

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

Path: task_types/tt_blastp_wnode_naming.cwl

Branch/Commit ID: 0514ffe248dd11068a3f2268bc67b6ce5ab051d2
workflow graph Varscan Workflow

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

Path: definitions/subworkflows/varscan_germline.cwl

Branch/Commit ID: 2e0562a5c3cd7aac24af4c622a5ae68a7fb23a71
workflow graph scRNA-seq pipeline using Salmon and Alevin

https://github.com/hubmapconsortium/salmon-rnaseq.git

Path: pipeline.cwl

Branch/Commit ID: fdde24c1c7bef16b727f26e7c98b6885c398550f
workflow graph Convert FastJs to cgfs

https://github.com/curoverse/l7g.git

Path: cwl-version/masterworkflow/fastj2cgf-wf.cwl

Branch/Commit ID: cdfe9178ad4e481d2391cd2da74b82d66a61b0bb
workflow graph count-lines9-wf.cwl

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

Path: tests/count-lines9-wf.cwl

Branch/Commit ID: 6397014050177074c9ccd0d771577f7fa9f728a3
workflow graph exome alignment and germline variant detection

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

Path: definitions/subworkflows/germline_detect_variants.cwl

Branch/Commit ID: 77ec4f26eb14ed82481828bd9f6ef659cfd8b40f
workflow graph idr.cwl

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

Path: workflows/ChIP-Seq/idr.cwl

Branch/Commit ID: e541470bc9d0b064bc4ed7dd2b45d8ec67760613
workflow graph Run genomic CMsearch

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

Path: bacterial_noncoding/wf_gcmsearch.cwl

Branch/Commit ID: e2a6cbcc36212433d8fbc804919442787a5e2a49