Explore Workflows

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

Graph Name Retrieved From View
workflow graph Decompress

Decompress mate pair fastq files

 https://github.com/MG-RAST/amplicon.git

Path: CWL/Workflows/decompress_mate_pair.workflow.cwl

Branch/Commit ID: 107cdd243d21449459a2126ddc7a365da64a74c0
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: 8a92669a566589d80fde9d151054ffc220ed4ddd
workflow graph pipeline.cwl#openoil_pipeline

Animation of an oil spill with openoil

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

Path: openoil/pipeline.cwl

Branch/Commit ID: f67eb693f0b078fddfd51cc0723ae77e3420e58c

Packed ID: openoil_pipeline
workflow graph Water bodies detection based on NDWI and otsu threshold

Water bodies detection based on NDWI and otsu threshold

 https://github.com/Terradue/ogc-eo-application-package-hands-on.git

Path: water-bodies/app-package.cwl

Branch/Commit ID: b080baffa34dc5d090d15ecf7eada388db73e4d2

Packed ID: water_bodies
workflow graph gathered exome alignment and somatic variant detection for cle purpose

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

Path: definitions/pipelines/gathered_cle_somatic_exome.cwl

Branch/Commit ID: 0805e8e0d358136468e0a9f49e06005e41965adc
workflow graph gk-full-step-siesta.cwl

https://github.com/vdikan/cwl-gk-thermal.git

Path: cwl/gk-full-step-siesta.cwl

Branch/Commit ID: 1415029b9bf5c90a644055c7708a9b99bd110241
workflow graph kmer_cache_retrieve

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

Path: task_types/tt_kmer_cache_retrieve.cwl

Branch/Commit ID: 4ea5956bb97ea2eb6de124bc9b6a6a81a14fd2e7
workflow graph wf-loadContents.cwl

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

Path: tests/wf-loadContents.cwl

Branch/Commit ID: b1d4a69df86350059bd49aa127c02be0c349f7de
workflow graph 1st-workflow.cwl

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

Path: tests/wf/1st-workflow.cwl

Branch/Commit ID: 5c7799a145595323d0a8628be1fe0e24985e793a
workflow graph Retrieval of genomes using the GCA identifiers from ENA

Runs the genome retrieval application with genome identifiers from the European Nucleotide Archive

https://git.wageningenur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_ena_retrieval.cwl

Branch/Commit ID: d6893a25b58b9b25fb76c5e060974b54d9eabc41