Explore Workflows

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

Graph Name Retrieved From View
workflow graph BLASTP, parse, dump FASTA

https://github.com/ncbi/cwl-demos.git

Path: blast-pipelines/simple_three_step.cwl

Branch/Commit ID: master
workflow graph alignment_bwa_mem.cwl

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/harmonization/alignment_bwa_mem.cwl

Branch/Commit ID: master
workflow graph Filter ChIP/ATAC peaks for Tag Density Profile or Motif Enrichment analyses

Filters ChIP/ATAC peaks with the neatest genes assigned for Tag Density Profile or Motif Enrichment analyses ============================================================================================================ Tool filters output from any ChIP/ATAC pipeline to create a file with regions of interest for Tag Density Profile or Motif Enrichment analyses. Peaks with duplicated coordinates are discarded.

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

Path: workflows/filter-peaks-for-heatmap.cwl

Branch/Commit ID: 7ced5a5259dbd8b3fc64456beaeffd44f4a24081
workflow graph js-expr-req-wf.cwl#wf

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

Path: testdata/js-expr-req-wf.cwl

Branch/Commit ID: 0ad6983898f0d9001fe0f416f97c4d8b940e384a

Packed ID: wf
workflow graph scatter-wf4.cwl#main

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

Path: tests/wf/scatter-wf4.cwl

Branch/Commit ID: 31aa094dce60cbb176229d6b918bfd5ae09c0390

Packed ID: main
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: af468ae34c82dc88399aeedfd8f12f1e87052367
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: 34d0ad68878b24aa1ffd8d8b8f7b8b2f5fd82787
workflow graph extract_gencoll_ids

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

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: ca75d68eb74c93b35b404ec7908dc5b260e16466
workflow graph pipeline-se.cwl

ATAC-seq pipeline - reads: SE

 https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/ATAC-seq_pipeline/pipeline-se.cwl

Branch/Commit ID: 3a4314c66c1eb090e656af5a0d388cec87d65318
workflow graph analysis for assembled sequences

rna / protein - qc, annotation, index, abundance

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/assembled.workflow.cwl

Branch/Commit ID: 49e29dfc5b1f7a7630831a1052f9136caa29dbf7