Explore Workflows

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

Graph Name Retrieved From View
workflow graph exome alignment with qc, no bqsr, no verify_bam_id

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

Path: definitions/pipelines/alignment_exome_mouse.cwl

Branch/Commit ID: 0db1a5f1ceedd4416ac550787c27b99c87dbe985
workflow graph chip-seq-alignment.cwl

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

Path: workflows/ChIP-Seq/chip-seq-alignment.cwl

Branch/Commit ID: 1b1cb5bbbe53a2dd5d7de7cdbff19c1bdbe23a49
workflow graph Chipseq alignment for mouse with qc and creating homer tag directory

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

Path: definitions/pipelines/chipseq_alignment_mouse.cwl

Branch/Commit ID: 0db1a5f1ceedd4416ac550787c27b99c87dbe985
workflow graph Salmon quantification, FASTQ -> H5AD count matrix

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

Path: steps/salmon-quantification.cwl

Branch/Commit ID: d71be688b76ed09a64cf5d8cf36182fe35cce6b3
workflow graph Merge, annotate, and generate a TSV for SVs

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

Path: definitions/subworkflows/merge_svs.cwl

Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46
workflow graph Exome QC workflow

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

Path: definitions/subworkflows/qc_exome.cwl

Branch/Commit ID: ae79bc51e8b502164dbe74ea3b068d6d4d36a1f8
workflow graph Subworkflow that runs cnvkit in single sample mode and returns a vcf file

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

Path: definitions/subworkflows/cnvkit_single_sample.cwl

Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46
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: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46
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