Explore Workflows

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

Graph Name Retrieved From View
workflow graph fp_filter workflow

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

Path: definitions/subworkflows/fp_filter.cwl

Branch/Commit ID: 1a908acc8059c2381ed146c6be1668f4bf1cfa73
workflow graph 03-map-se.cwl

ChIP-seq 03 mapping - reads: SE

 https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/ChIP-seq_pipeline/03-map-se.cwl

Branch/Commit ID: 4636f2c1a8bcfceeb4b3596ee29e9c06311ed4a1
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: 104059e07a2964673e21d371763e33c0afeb2d03
workflow graph io-union-input-default-wf.cwl

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

Path: v1.0/v1.0/io-union-input-default-wf.cwl

Branch/Commit ID: 46947322eb5a99940eb3b5d3088e58f5189398e7
workflow graph 04-quantification-se-revstranded.cwl

RNA-seq 04 quantification

 https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/RNA-seq_pipeline/04-quantification-se-revstranded.cwl

Branch/Commit ID: 4636f2c1a8bcfceeb4b3596ee29e9c06311ed4a1
workflow graph HS Metrics workflow

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

Path: definitions/subworkflows/hs_metrics.cwl

Branch/Commit ID: 8eb189a4a34dc8cd86380685f814c79a444a7601
workflow graph conflict-wf.cwl#collision

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

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

Branch/Commit ID: 84939620c3eec1ab11369849c63237ebfa48da41

Packed ID: collision
workflow graph pipeline-pe-blacklist-removal.cwl

ATAC-seq pipeline - reads: PE - with blacklist removal

 https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/ATAC-seq_pipeline/pipeline-pe-blacklist-removal.cwl

Branch/Commit ID: 4636f2c1a8bcfceeb4b3596ee29e9c06311ed4a1
workflow graph 03-map-pe.cwl

ChIP-seq 03 mapping - reads: PE

 https://github.com/Duke-GCB/GGR-cwl.git

Path: v1.0/ChIP-seq_pipeline/03-map-pe.cwl

Branch/Commit ID: ebd63f705d0fde7290e42c8300d5420c25cfbfe3
workflow graph Chipseq alignment with qc and creating homer tag directory

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

Path: definitions/pipelines/chipseq.cwl

Branch/Commit ID: 049f4aeff4c4a1b8421cac9b1c1c1f0da5848315