Explore Workflows

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

Graph Name Retrieved From View
workflow graph collapsed_fastq_to_bam.cwl

https://github.com/mskcc/Innovation-Pipeline.git

Path: workflows/marianas/collapsed_fastq_to_bam.cwl

Branch/Commit ID: 9998da2da694af2edad7c2135f6995e2282794a3
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: 12c29f88855329192bfff977f046990031f04931
workflow graph advanced-header.cwl

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

Path: metadata/advanced-header.cwl

Branch/Commit ID: e7a896db41063c52197aec8d5b49ed013d7a5ba7
workflow graph kmer_cache_store

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: f5c11df465aaadf712c38ba4933679fe1cbe03ca
workflow graph group-isoforms-batch.cwl

Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored.

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

Path: tools/group-isoforms-batch.cwl

Branch/Commit ID: 1131f82a53315cca217a6c84b3bd272aa62e4bca
workflow graph count-lines9-wf-noET.cwl

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

Path: tests/count-lines9-wf-noET.cwl

Branch/Commit ID: 86c46cb397de029e4c91f02cca40fa2b54d22f37
workflow graph duplicated_readgroup_fix.cwl

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/utils/duplicated_readgroup_fix.cwl

Branch/Commit ID: 286bce04c474d28bddeb7dbe43ab8d59919fe855
workflow graph kmer_top_n_extract

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

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: 7319ccfd2108929588bdc266d9df198629dfaa65
workflow graph kf_alignment_optimized_wf

https://github.com/inab/vre_cwl_executor.git

Path: tests/basic/data/workflows/basic_example_3.cwl

Branch/Commit ID: 00d6c35e3932bef3906a9158939cc0b74bea2dda
workflow graph umi duplex alignment fastq workflow

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

Path: definitions/pipelines/alignment_umi_duplex.cwl

Branch/Commit ID: 061d3a2fbcd8a1c39c0b38c549e528deb24a9d54