Explore Workflows

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

Graph Name Retrieved From View
workflow graph clipAteam.cwl

https://github.com/lonbar/VLBI-cwl.git

Path: workflows/clipAteam.cwl

Branch/Commit ID: 58d6c7fe14e9a4de4e1659f8eedd2ca527c18a28
workflow graph HS Metrics workflow

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

Path: definitions/subworkflows/hs_metrics.cwl

Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46
workflow graph Long-covid.cwl

https://github.com/cwlviewer-test/Long-covid---aedea650-7a21-11ed-b9d2-e51f21933d80.git

Path: Long-covid.cwl

Branch/Commit ID: e6e351cba4bf23073daa00364da5290d3c87738e
workflow graph Dockstore.cwl

https://github.com/LinkunGao/dock-workflow.git

Path: Dockstore.cwl

Branch/Commit ID: 4abae37d554d8a58c146d85544cd3c4d71b200d3
workflow graph genomics-workspace-transcript.cwl

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: flow_genomicsWorkspace/genomics-workspace-transcript.cwl

Branch/Commit ID: 5910b4d88aca172252d9102ddb610a7dc9e1347f
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: 472d453995dcda1b66884c31db562f4fb6094e5a
workflow graph main.cwl

https://github.com/alpha-unito/cwl-1000genome-workflow.git

Path: main.cwl

Branch/Commit ID: 77aaa24c2576826a9a11380b70e84507a53081e8
workflow graph count-lines7-wf_v1_1.cwl

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

Path: testdata/count-lines7-wf_v1_1.cwl

Branch/Commit ID: 139c64b55f7693d22e6646b8afe585f90da11dcb
workflow graph STAR-Alignment-PE

This workflow aligns the fastq files using STAR for paired-end samples

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

Path: workflows/Alignments/star-alignment.cwl

Branch/Commit ID: 1b1cb5bbbe53a2dd5d7de7cdbff19c1bdbe23a49
workflow graph exome alignment with qc, no bqsr, no verify_bam_id

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

Path: definitions/pipelines/exome_alignment_mouse.cwl

Branch/Commit ID: 0805e8e0d358136468e0a9f49e06005e41965adc