Explore Workflows

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

Graph Name Retrieved From View
workflow graph Seed Search Compartments

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

Path: protein_alignment/wf_seed.cwl

Branch/Commit ID: 22ffe27d9d4a899def7592d75d5871c1856adbdb
workflow graph Filter Protein Alignments

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

Path: protein_alignment/wf_align_filter.cwl

Branch/Commit ID: 22ffe27d9d4a899def7592d75d5871c1856adbdb
workflow graph Run genomic CMsearch

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

Path: bacterial_noncoding/wf_gcmsearch.cwl

Branch/Commit ID: 22ffe27d9d4a899def7592d75d5871c1856adbdb
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: 2b8146f76595f0c4d8bf692de78b21280162b1d0
workflow graph step-valuefrom-wf.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/step-valuefrom-wf.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3
workflow graph QuantSeq 3' FWD, FWD-UMI or REV for single-read mRNA-Seq data

### Devel version of QuantSeq 3' FWD, FWD-UMI or REV for single-read mRNA-Seq data

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

Path: workflows/trim-quantseq-mrnaseq-se-strand-specific.cwl

Branch/Commit ID: 00ea05e22788029370898fd4c17798b11edf0e57
workflow graph dynresreq-workflow.cwl

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

Path: tests/dynresreq-workflow.cwl

Branch/Commit ID: 86c46cb397de029e4c91f02cca40fa2b54d22f37
workflow graph Seed Protein Alignments

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

Path: protein_alignment/wf_seed_1.cwl

Branch/Commit ID: 22ffe27d9d4a899def7592d75d5871c1856adbdb
workflow graph Filter Protein Seeds; Find ProSplign Alignments

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

Path: protein_alignment/wf_compart_filter_prosplign.cwl

Branch/Commit ID: 22ffe27d9d4a899def7592d75d5871c1856adbdb
workflow graph downsample unaligned BAM and align

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

Path: definitions/subworkflows/downsampled_alignment.cwl

Branch/Commit ID: dc2c019c1aa24cc01b451a0f048cf94a35f163c4