Explore Workflows

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

Graph Name Retrieved From View
workflow graph wf_get_peaks_scatter_se.cwl

The \"main\" workflow. Takes fastq files generated using the seCLIP protocol (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5991800/) and outputs candidate RBP binding regions (peaks). runs: wf_get_peaks_se.cwl through scatter across multiple samples.

https://github.com/YeoLab/eclip.git

Path: cwl/wf_get_peaks_scatter_se.cwl

Branch/Commit ID: b2b95f58f96ee5b34bd9b342d0ecda63d135e278
workflow graph fp_filter workflow

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

Path: definitions/subworkflows/fp_filter.cwl

Branch/Commit ID: 27dcb1ae121be6a23057b74332b8c752ea425735
workflow graph scatter GATK HaplotypeCaller over intervals

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

Path: definitions/subworkflows/gatk_haplotypecaller_iterator.cwl

Branch/Commit ID: bed420556091b7b8b45cf20a95e5947e1de9a416
workflow graph wf_demultiplex_pe.cwl

https://github.com/YeoLab/eclip.git

Path: cwl/wf_demultiplex_pe.cwl

Branch/Commit ID: 6b533898c395e9e5b9d0acc1587d0c68bc56abe0
workflow graph Filter single sample sv vcf from paired read callers(Manta/Smoove)

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

Path: definitions/subworkflows/sv_paired_read_caller_filter.cwl

Branch/Commit ID: 06d2440d115b446c299b4ce96e8812d2f8df86ec
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: e9c83739a93fa0b18f8dea2f98b632a9e32725c9
workflow graph grep-and-count-for-figure-1.cwl

https://github.com/manabuishii/cwl-samples.git

Path: grep-and-count-for-figure-1.cwl

Branch/Commit ID: bee68ab4a890e552ab341558a305206b5f310a73
workflow graph Per-region pindel

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

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: 844c10a4466ab39c02e5bfa7a210c195b8efa77a
workflow graph exome_metrics.cwl

https://github.com/NCI-GDC/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/exome_metrics.cwl

Branch/Commit ID: 1046947f8d2923e6563b3aceac9e435554c5bea1
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: 1f03ff02ef829bdb9d582825bcd4ca239e84ca2e