Explore Workflows

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

Graph Name Retrieved From View
workflow graph bam_readcount workflow

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

Path: definitions/subworkflows/bam_readcount.cwl

Branch/Commit ID: d2c2f2eb846ae2e9cdcab46e3bb88e42126cb3f5
workflow graph Varscan Workflow

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

Path: definitions/subworkflows/varscan_germline.cwl

Branch/Commit ID: ad65dc1dfff9afa5077f498b85e699716c47f6cb
workflow graph fasta2taxa-plot

Input is a fasta file with n>1 samples, with sample id as sequence identifier prefix, and a sample id file. The workflow calls open otus and assigns taxa using greengenes. The output are taxa plots.

https://github.com/MG-RAST/qiime-pipeline.git

Path: CWL/Workflows/qiime/join-reads2reference2plot.cwl

Branch/Commit ID: 3565f6f4d26f5709aff56e6a266dbb7c7d6129d8
workflow graph Exome QC workflow

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

Path: definitions/subworkflows/qc_exome_no_verify_bam.cwl

Branch/Commit ID: dc2c019c1aa24cc01b451a0f048cf94a35f163c4
workflow graph Subworkflow to allow calling different SV callers which require bam files as inputs

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

Path: definitions/subworkflows/single_sample_sv_callers.cwl

Branch/Commit ID: efbbe5ed51f6ac583e87a348785c72818a33f56e
workflow graph running cellranger mkfastq and count

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

Path: definitions/subworkflows/cellranger_mkfastq_and_count.cwl

Branch/Commit ID: efbbe5ed51f6ac583e87a348785c72818a33f56e
workflow graph original.cwl#main_pipeline

Simulation steps pipeline

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

Path: workflow_in_workflow/original.cwl

Branch/Commit ID: cb62ab53f349bf64e880199d1e148439ebe456c1

Packed ID: main_pipeline
workflow graph 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: dda6e8b5ada3f106a2b3bfcc1b151eccf9977726
workflow graph rRNA_selection.cwl

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: tools/rRNA_selection.cwl

Branch/Commit ID: 19fce22aa01f8d7d068dc7f11f5e0a3bdb9cf854
workflow graph Viral contig assign

https://github.com/EBI-Metagenomics/emg-viral-pipeline.git

Path: cwl/src/Tools/Assign/assign_swf.cwl

Branch/Commit ID: b0ed3f07c8faced85609287759596ad83e154977