Explore Workflows

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

Path: pindel/pindel_cat.cwl

Branch/Commit ID: 6eb7d35ad46207f4ff49e84106b717e17331eb4b

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

Path: workflows/kfdrc_sentieon_alignment_wf.cwl

Branch/Commit ID: e75f0c96153a484db1f882f6ff2a9764519a3179

Simulation steps pipeline

https://github.com/ILIAD-ocean-twin/application_package.git

Path: workflow_in_workflow/original.cwl

Branch/Commit ID: aab1b560c6a855c645f43635f155a15800a7ce0d

Packed ID: main_pipeline

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

Path: tests/wf/mut.cwl

Branch/Commit ID: bbe20f54deea92d9c9cd38cb1f23c4423133d3de

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

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

Branch/Commit ID: 3ed10d0ea7ac57550433a89a92bdbe756bdb0e40

Packed ID: main

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

Path: definitions/pipelines/bisulfite.cwl

Branch/Commit ID: e2a34d2b8c406db9aed8e49e8bdcf36f51444379

Creates indices for: * [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) * [bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) It performs the following steps: 1. `STAR --runMode genomeGenerate` to generate indices, based on [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) and [GTF](http://mblab.wustl.edu/GTF2.html) input files, returns results as an array of files 2. Outputs indices as [Direcotry](http://www.commonwl.org/v1.0/CommandLineTool.html#Directory) data type 3. Separates *chrNameLength.txt* file from Directory output 4. `bowtie-build` to generate indices requires genome [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) file as input, returns results as a group of main and secondary files

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

Path: workflows/genome-indices.cwl

Branch/Commit ID: 91bb63948c0a264334b9007ef85f936768d90d11

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: e89b2c17aa5efccef6ca424dec5a0a021bd8d20c

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

Path: tests/record-in-secondaryFiles-wf.cwl

Branch/Commit ID: e515226f8ac0f7985cd94dae4a301150adae3050

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

Path: workflow/kfdrc_star_diploid_wf.cwl

Branch/Commit ID: 3c8e721d47d68035e4d4f55fa0a2eede18c6e9da