Explore Workflows

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

Graph Name Retrieved From View
workflow graph Detect Docm variants

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

Path: definitions/subworkflows/docm_cle.cwl

Branch/Commit ID: b9e7392e72506cadd898a6ac4db330baf6535ab6
workflow graph Raw sequence data to BQSR

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

Path: definitions/subworkflows/sequence_to_bqsr.cwl

Branch/Commit ID: 7638b3075863ae8172f4adaec82fb2eb8e80d3d5
workflow graph pipeline.cwl

https://github.com/hubmapconsortium/ome-tiff-pyramid.git

Path: pipeline.cwl

Branch/Commit ID: b1b40c45741a60e643312ab5513086dbb8105e9a
workflow graph kfdrc_cram_reheader_wf.cwl

https://github.com/kids-first/kf-alignment-workflow.git

Path: workflows/kfdrc_cram_reheader_wf.cwl

Branch/Commit ID: a25fbec152d701623a7a8fa494b1179cc3c39c38
workflow graph 02-trim-se.cwl

ATAC-seq 02 trimming - reads: SE

 https://github.com/Duke-GCB/GGR-cwl.git

Path: v1.0/ATAC-seq_pipeline/02-trim-se.cwl

Branch/Commit ID: 487af88ef0b971f76ecd1a215639bb47e3ee94e1
workflow graph amplicon_preprocess_workflow.cwl

https://github.com/kmooog/amplicon-pipeline.git

Path: script/1-preproccess/amplicon_preprocess_workflow.cwl

Branch/Commit ID: eccef9b8e80e1a8729e7bd54f06f895a847b024d
workflow graph Apply filters to VCF file

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

Path: definitions/subworkflows/filter_vcf.cwl

Branch/Commit ID: ece70ac30cd87100a70f7dc64d08fa72724e9416
workflow graph gathered exome alignment and somatic variant detection

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

Path: definitions/pipelines/somatic_exome_gathered.cwl

Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a
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: 8049a781ac4aae579fbd3036fa0bf654532f15be
workflow graph kmer_build_tree

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

Path: task_types/tt_kmer_build_tree.cwl

Branch/Commit ID: a539d600357a48a558daf43fc41a89aae79f9e86