Explore Workflows

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

Graph Name Retrieved From View
workflow graph pindel parallel workflow

https://github.com/genome/cancer-genomics-workflow.git

Path: pindel/workflow.cwl

Branch/Commit ID: 6eb7d35ad46207f4ff49e84106b717e17331eb4b
workflow graph strelka workflow

https://github.com/genome/cancer-genomics-workflow.git

Path: strelka/workflow.cwl

Branch/Commit ID: 6eb7d35ad46207f4ff49e84106b717e17331eb4b
workflow graph Varscan Workflow

https://github.com/genome/cancer-genomics-workflow.git

Path: varscan/workflow.cwl

Branch/Commit ID: 6eb7d35ad46207f4ff49e84106b717e17331eb4b
workflow graph diadem_workflow_test1.cwl

https://github.com/cnherrera/CWL_Workflow_DIADEM_use_case.git

Path: diadem_workflow_test1.cwl

Branch/Commit ID: 2932d26107eb418c1adf865cc7c13c147a6ed71d
workflow graph checker_workflow_wrapping_workflow.cwl

This demonstrates how to wrap a \"real\" workflow with a checker workflow that runs both the tool and a tool that performs verification of results

https://github.com/dockstore-testing/dockstore-workflow-md5sum-unified.git

Path: checker_workflow_wrapping_workflow.cwl

Branch/Commit ID: 3a604c0e70b2dc62973917cc186dc6db5a6ce519
workflow graph scatter-valuefrom-wf5.cwl

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf5.cwl

Branch/Commit ID: bbe20f54deea92d9c9cd38cb1f23c4423133d3de
workflow graph Subworkflow to allow calling cnvkit with cram instead of bam files

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

Path: definitions/subworkflows/cram_to_cnvkit.cwl

Branch/Commit ID: a23f42ef49c10a588fd35a3afaad5de03e253533
workflow graph format_rrnas_from_seq_entry

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

Path: task_types/tt_format_rrnas_from_seq_entry.cwl

Branch/Commit ID: e71779665f42fcf34601b0f65e030bb0dd47fa79
workflow graph kmer_top_n_extract

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

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: 1b8d71c75156a1a62bf0477d59db26010e2dcc29
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: b5e16e359007150647b14dc6e038f4eb8dccda79