Explore Workflows

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

Graph Name Retrieved From View
workflow graph kmer_ref_compare_wnode

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

Path: task_types/tt_kmer_ref_compare_wnode.cwl

Branch/Commit ID: 1a6b9e5dea09caa0debbaff30ca39005dfa5e4d4
workflow graph 1st-workflow.cwl

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

Path: v1.0/examples/1st-workflow.cwl

Branch/Commit ID: e152deebf9777ec75aeb6edb884bdeb1d9008b1a
workflow graph varscan somatic workflow

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

Path: definitions/subworkflows/varscan.cwl

Branch/Commit ID: d3e4bf55753cd92f97537c7d701187ea92d1e5f0
workflow graph transform.cwl

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

Path: workflows/dnaseq/validate/transform.cwl

Branch/Commit ID: 1046947f8d2923e6563b3aceac9e435554c5bea1
workflow graph Align reference proteins plane complete workflow

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

Path: protein_alignment/wf_protein_alignment.cwl

Branch/Commit ID: 5ec226c941562124032ca6861bc8d1aeabf9d91a
workflow graph wf_demultiplex_pe.cwl

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

Path: cwl/wf_demultiplex_pe.cwl

Branch/Commit ID: b2b95f58f96ee5b34bd9b342d0ecda63d135e278
workflow graph assm_assm_blastn_wnode

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

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: 69c0f25d08cfa02d8bfaa85ce5d70dd14cc52e3f
workflow graph Run genomic CMsearch (Rfam rRNA)

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

Path: bacterial_ncrna/wf_gcmsearch.cwl

Branch/Commit ID: 5ec226c941562124032ca6861bc8d1aeabf9d91a
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: 77970404d7c704cba965ae646582e19e5d76aabe
workflow graph Bacterial Annotation, pass 2, blastp-based functional annotation (first pass)

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

Path: bacterial_annot/wf_bacterial_annot_pass2.cwl

Branch/Commit ID: 5ec226c941562124032ca6861bc8d1aeabf9d91a