Explore Workflows

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

Graph Name Retrieved From View
workflow graph bam to trimmed fastqs and biscuit alignments

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl

Branch/Commit ID: 60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2
workflow graph scatter-valuefrom-inputs-wf1.cwl

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

Path: tests/scatter-valuefrom-inputs-wf1.cwl

Branch/Commit ID: 50251ef931d108c09bed2d330d3d4fe9c562b1c3
workflow graph wf.cwl

https://github.com/ResearchObject/runcrate.git

Path: tests/data/no-output-run-1/snapshot/wf.cwl

Branch/Commit ID: 44c831fb97958470d88efc8ecf7ff09bfa2c4e1a
workflow graph kallisto_scatter_synapse_single_end_workflow.cwl

https://github.com/CRI-iAtlas/iatlas-workflows.git

Path: Kallisto/workflow/kallisto_scatter_synapse_single_end_workflow.cwl

Branch/Commit ID: c7fa0fa9ef94c657b664f680462dbc3f5b7a32e8
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: a402541b8530f30eab726c160da90a23036847a1
workflow graph Generate genome indices for STAR & bowtie

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: 46a077b51619c6a14f85e0aa5260ae8a04426fab
workflow graph Cellranger Reanalyze

Cellranger Reanalyze ====================

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

Path: workflows/cellranger-reanalyze.cwl

Branch/Commit ID: f3e44d3b0f198cf5245c49011124dc3b6c2b06fd
workflow graph tt_blastn_wnode

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: d218e081d8f6a4fdab56a38ce0fc2fae6216cecc
workflow graph mut.cwl

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

Path: tests/wf/mut.cwl

Branch/Commit ID: ec2cf2da6c31ffedf827a0fb213b5204e172f510
workflow graph Filter differentially expressed genes from DESeq for Tag Density Profile Analyses

Filters differentially expressed genes from DESeq for Tag Density Profile Analyses ================================================================================== Tool filters output from DESeq pipeline run for genes to create a file with regions of interest for Tag Density Profile Analyses.

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

Path: workflows/filter-deseq-for-heatmap.cwl

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f