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: ad948b2691ef7f0f34de38f0102c3cd6f5182b29
workflow graph Unaligned to aligned BAM

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

Path: definitions/subworkflows/align.cwl

Branch/Commit ID: 2979b565f88ceebca934611adbf3fb8cefd65a19
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: 3a287b7cb6162cdea79865235d224fea45963d87
workflow graph Add snv and indel bam-readcount files to a vcf

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

Path: definitions/subworkflows/vcf_readcount_annotator.cwl

Branch/Commit ID: 480c438a6a7e78c624712aec01bc4214d2bc179c
workflow graph rhapsody_targeted_1.8.cwl#SplitAndSubsample.cwl

SplitAndSubsample splits, subsamples and formats read files to be deposited in QualityFilter.

https://github.com/longbow0/cwl.git

Path: v1.8/rhapsody_targeted_1.8.cwl

Branch/Commit ID: b9ec66d82bc04934fbe9f9088ae7e802d72c4a4e

Packed ID: SplitAndSubsample.cwl
workflow graph rhapsody_targeted_1.8.cwl#UncompressDatatables.cwl

https://github.com/longbow0/cwl.git

Path: v1.8/rhapsody_targeted_1.8.cwl

Branch/Commit ID: b9ec66d82bc04934fbe9f9088ae7e802d72c4a4e

Packed ID: UncompressDatatables.cwl
workflow graph process VCF workflow

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

Path: definitions/subworkflows/strelka_process_vcf.cwl

Branch/Commit ID: b9e7392e72506cadd898a6ac4db330baf6535ab6
workflow graph Pairwise genomic regions intersection

Pairwise genomic regions intersection ============================================= Overlaps peaks from two ChIP/ATAC experiments

 https://github.com/datirium/workflows.git

Path: workflows/peak-intersect.cwl

Branch/Commit ID: 4a5c59829ff8b9f3c843e66e3c675dcd9c689ed5
workflow graph exome alignment with qc

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

Path: definitions/pipelines/alignment_exome.cwl

Branch/Commit ID: 04d21c33a5f2950e86db285fa0a32a6659198d8a
workflow graph make_final_outputs_workflow.cwl

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

Path: workflows/subworkflows/rnaseq_processing/make_final_outputs_workflow.cwl

Branch/Commit ID: f0594206c230e53ad3ad9de14364fc6bce1d5cb7