Explore Workflows

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

Graph Name Retrieved From View
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: 549fac35bf6b8b1c25af0f4f6c3f162c40dc130e
workflow graph basename-fields-test.cwl

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

Path: cwltool/schemas/v1.0/v1.0/basename-fields-test.cwl

Branch/Commit ID: bfe56f3138e9e6fc0b9b8c06447553d4cea03d59
workflow graph wgs alignment and tumor-only variant detection

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

Path: definitions/pipelines/wgs.cwl

Branch/Commit ID: ae75b938e6e8ae777a55686bbacad824b3c6788c
workflow graph exome alignment and germline variant detection

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

Path: definitions/subworkflows/germline_detect_variants.cwl

Branch/Commit ID: 5be54bf09092c53e6c7797a875f64a360d511d7f
workflow graph Varscan Workflow

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

Path: definitions/subworkflows/varscan_germline.cwl

Branch/Commit ID: 7b4b489474473c3d2d992a838b89632c2b97dc2c
workflow graph umi molecular alignment workflow

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

Path: definitions/subworkflows/molecular_alignment.cwl

Branch/Commit ID: 31a179d7a2f2ac86bfd7fcc4dc79832c3739ae76
workflow graph workflow.cwl

https://github.com/ashviyer/PSVD-transcriptomics-workflow.git

Path: workflow/workflow.cwl

Branch/Commit ID: 65800209da48a28eaa5d120605c8c6749eb6d8b9
workflow graph Cell Ranger ARC Aggregate

Cell Ranger ARC Aggregate =========================

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

Path: workflows/cellranger-arc-aggr.cwl

Branch/Commit ID: 12e5256de1b680c551c87fd5db6f3bc65428af67
workflow graph exomeseq-gatk4-01-preprocessing.cwl

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

Path: subworkflows/exomeseq-gatk4-01-preprocessing.cwl

Branch/Commit ID: 727ad5dbd15ef6aaa9cd5a3f7b23e74ff74663ea
workflow graph umi per-lane alignment subworkflow

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

Path: definitions/subworkflows/umi_alignment.cwl

Branch/Commit ID: 5be54bf09092c53e6c7797a875f64a360d511d7f