Explore Workflows

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

Graph Name Retrieved From View
workflow graph search.cwl#main

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

Path: cwltool/schemas/v1.0/v1.0/search.cwl

Branch/Commit ID: 478c2ffc09fb189c4f36ccb82aad945b3db5f9b3

Packed ID: main
workflow graph Seed Protein Alignments I

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

Path: protein_alignment/wf_seed_1.cwl

Branch/Commit ID: 62464fecfe319398affdec50d46054a97466f61a
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: 954bb2f213d97dfef1cddaf9e830169a92ad0c6b
workflow graph scatter-wf1.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/scatter-wf1.cwl

Branch/Commit ID: b1d4a69df86350059bd49aa127c02be0c349f7de
workflow graph THOR - differential peak calling of ChIP-seq signals with replicates

What is THOR? -------------- THOR is an HMM-based approach to detect and analyze differential peaks in two sets of ChIP-seq data from distinct biological conditions with replicates. THOR performs genomic signal processing, peak calling and p-value calculation in an integrated framework. For more information please refer to: ------------------------------------- Allhoff, M., Sere K., Freitas, J., Zenke, M., Costa, I.G. (2016), Differential Peak Calling of ChIP-seq Signals with Replicates with THOR, Nucleic Acids Research, epub gkw680.

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

Path: workflows/rgt-thor.cwl

Branch/Commit ID: 954bb2f213d97dfef1cddaf9e830169a92ad0c6b
workflow graph scatter-wf4.cwl#main

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

Path: cwltool/schemas/v1.0/v1.0/scatter-wf4.cwl

Branch/Commit ID: 478c2ffc09fb189c4f36ccb82aad945b3db5f9b3

Packed ID: main
workflow graph extract_file_with_index.cwl

https://github.com/NCI-GDC/aliquot-maf-cwl.git

Path: vcf-to-aliquot-maf/subworkflows/extract_file_with_index.cwl

Branch/Commit ID: 4c0c8a2a75634d4558904678644f1d2f0f0345e8
workflow graph amplicon_metrics.cwl

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

Path: workflows/bamfastq_align/amplicon_metrics.cwl

Branch/Commit ID: 20a901f44c9fb0e6f4ee3c40ec33fa4b1c8ef005
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: 5c40c5a0464c84076e0e407a0e05522b43bdc0a6
workflow graph format_rrnas_from_seq_entry

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

Path: task_types/tt_format_rrnas_from_seq_entry.cwl

Branch/Commit ID: 5e92165ac2c11608ab2db42fe2d66eabe72dbb40