Explore Workflows

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

Graph Name Retrieved From View
workflow graph bgzip and index VCF

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

Path: definitions/subworkflows/bgzip_and_index.cwl

Branch/Commit ID: 31602b94b34ff55876147c7299e1bec47e8d1a31
workflow graph kmer_gc_extract_wnode

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

Path: task_types/tt_kmer_gc_extract_wnode.cwl

Branch/Commit ID: e668f9c4047f1971ae53040a5af3eccc4bfc3c53
workflow graph ST520115.cwl

https://github.com/Marco-Salvi/dtc51.git

Path: ST520115.cwl

Branch/Commit ID: 272db37d2b8108a146769f0fb0383bb824c9788f
workflow graph Detect Docm variants

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

Path: definitions/subworkflows/docm_cle.cwl

Branch/Commit ID: 2f65fc96207a71b1cda4e246f808bed056608cd0
workflow graph Running cellranger count and lineage inference

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

Path: definitions/subworkflows/single_cell_rnaseq.cwl

Branch/Commit ID: 60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2
workflow graph fillout_workflow.cwl

Workflow to run GetBaseCountsMultiSample fillout on a number of bam files with a single maf file

https://github.com/mskcc/pluto-cwl.git

Path: cwl/fillout_workflow.cwl

Branch/Commit ID: 342e6f1f4f7a3839e579fbe96ccc8d6f7a61ac77
workflow graph Filter Protein Seeds I; Find ProSplign Alignments I

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

Path: protein_alignment/wf_compart_filter_prosplign.cwl

Branch/Commit ID: 0b036c0e52935eeb413c784e14275b87d5eb028e
workflow graph pindel parallel workflow

https://github.com/apaul7/cancer-genomics-workflow.git

Path: definitions/subworkflows/pindel.cwl

Branch/Commit ID: bfcb5ffbea3d00a38cc03595d41e53ea976d599d
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/Barski-lab/workflows.git

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: 852fa49a70fe0965de6892fa0832f30b710f0e75
workflow graph Seed Protein Alignments I

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

Path: protein_alignment/wf_seed_1.cwl

Branch/Commit ID: 0b036c0e52935eeb413c784e14275b87d5eb028e