Explore Workflows

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

Graph	Name	Retrieved From	View
	mut2.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/mut2.cwl Branch/Commit ID: 814bd0405a7701efc7d63e8f0179df394c7766f7
	env-wf2.cwl	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/env-wf2.cwl Branch/Commit ID: 7bfd77118cdc80dd7150115dd7a1a7ee6046f6fe
	Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/pvacseq.cwl Branch/Commit ID: aba52e94b6d7470132d3c092c26d67e29d615300
	Build STAR indices Workflow runs [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) to build indices for reference genome provided in a single FASTA file as fasta_file input and GTF annotation file from annotation_gtf_file input. Generated indices are saved in a folder with the name that corresponds to the input genome.	https://github.com/datirium/workflows.git Path: workflows/star-index.cwl Branch/Commit ID: bf80c9339d81a78aefb8de661bff998ed86e836e
	AcceptParameterFailure validation or review of parameter updates failed. Action required and feedback to be provided.	https://github.com/gammasim/workflows.git Path: workflows/AcceptParameterFailure.cwl Branch/Commit ID: 789752af87eb190387ff2acb4c95c7a5cdb961e7
	trim-rnaseq-pe.cwl Runs RNA-Seq BioWardrobe basic analysis with pair-end data file.	https://github.com/Barski-lab/workflows.git Path: workflows/trim-rnaseq-pe.cwl Branch/Commit ID: 812b0ff40dda18ab7a9a872ff13a577be8531ba6
	Quality assessment, amplicon classification and functional prediction Workflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps: - FastQC (read quality control) - NGTax 2.0 - Picrust 2 - Export module for ngtax	https://git.wur.nl/unlock/cwl.git Path: cwl/workflows/workflow_ngtax_picrust2.cwl Branch/Commit ID: 2242521957bb07fc589d6bb07046f6a166bc975a
	animal-genome-assembly.with_canu.cwl Animal Genome Assembly pipeline by Kazuharu Arakawa (@gaou_ak), CWLized by Tazro Ohta (@inutano). This workflow contains assembly step by canu which may take a few weeks to complete. Be careful to run!	https://github.com/pitagora-network/DAT2-cwl.git Path: workflow/animal-genome-assembly/animal-genome-assembly.with_canu.cwl Branch/Commit ID: b63171820f546def8c26f558182912a71af88b48
	exomeseq-01-preprocessing.cwl	https://github.com/Duke-GCB/bespin-cwl.git Path: subworkflows/exomeseq-01-preprocessing.cwl Branch/Commit ID: 727ad5dbd15ef6aaa9cd5a3f7b23e74ff74663ea
	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: 94c6ea7bf4b64599746d778568efbd8e10f0d5ba