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: 87f213456b3f966b773d396cce1fe5a272dad858
workflow graph hi-c-processing-bam.cwl

https://github.com/4dn-dcic/docker-4dn-hic.git

Path: cwl/hi-c-processing-bam.cwl

Branch/Commit ID: a0d5318c07793cb7d841387d13b026dedc7f0496
workflow graph protein_extract

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

Path: progs/protein_extract.cwl

Branch/Commit ID: 96dbb414d287f4382e2d477fb1851aeaa5f14f2b
workflow graph Salmon quantification, FASTQ -> H5AD count matrix

https://github.com/hubmapconsortium/salmon-rnaseq.git

Path: steps/salmon-quantification.cwl

Branch/Commit ID: 53dc83aff682e69943cc41d711a3765d2a5b0413
workflow graph nontrivial.cwl

https://github.com/dockstore-testing/tooltester-wes-testing.git

Path: nontrivial/nontrivial.cwl

Branch/Commit ID: fffba729abe4a1ea6b8b23d95b7a6b56c3d20114
workflow graph Deprecated. AltAnalyze Build Reference Indices

Deprecated. AltAnalyze Build Reference Indices

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

Path: workflows/altanalyze-prepare-genome.cwl

Branch/Commit ID: fc45b83b3edd8378e14bce3de14f3eb6d4a140dc
workflow graph Get Proteins

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

Path: wf_bacterial_prot_src.cwl

Branch/Commit ID: 96dbb414d287f4382e2d477fb1851aeaa5f14f2b
workflow graph alignment for mouse with qc

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

Path: definitions/pipelines/alignment_wgs_mouse.cwl

Branch/Commit ID: 0db1a5f1ceedd4416ac550787c27b99c87dbe985
workflow graph workflow.cwl

https://github.com/Andreja28/cloud-workflows.git

Path: cwl/torso/workflow.cwl

Branch/Commit ID: ed5dd0589aa951193f4b98f44b0edc7f58e04ba5
workflow graph exome alignment and germline variant detection

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

Path: definitions/subworkflows/germline_detect_variants.cwl

Branch/Commit ID: ae79bc51e8b502164dbe74ea3b068d6d4d36a1f8