Explore Workflows

Star/HTSeq RNA Seq Pipeline

https://github.com/Duke-GCB/bespin-cwl.git

Path: workflows/rnaseq-pt1.cwl

Branch/Commit ID: master

Calculates the rescue ratio (see Gabe's protocols paper), given two eCLIP IP samples and 2 size-matched input samples. Also returns the reproducible peaks given these two samples. This is different from the 1input workflow in that each INPUT is first merged together and is used downstream instead of the 1input version, which remains unmodified. Merged inputs are NOT used in calculating true reproducible peaks.

https://github.com/YeoLab/merge_peaks.git

Path: cwl/wf_rescue_ratio_2inputs.cwl

Branch/Commit ID: master

https://github.com/hubmapconsortium/codex-pipeline.git

Path: pipeline.cwl

Branch/Commit ID: 221f7c4

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

Path: tools/collate_unique_SSU_headers.cwl

Branch/Commit ID: 8515542

https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/sra/download_quality_control.cwl

Branch/Commit ID: master

create STAR index for mapping CAGE-Seq data (step 1: decompress reference genome fasta file, step 2: create STAR index)

https://github.com/RyoNozu/CWL4IncorporateTSSintoGXF.git

Path: workflow/02_star_index_subworkflow.cwl

Branch/Commit ID: main

https://github.com/hubmapconsortium/sprm.git

Path: pipeline.cwl

Branch/Commit ID: 62d3a80

ChIP-seq 02 trimming - reads: PE

https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/ChIP-seq_pipeline/02-trim-pe.cwl

Branch/Commit ID: master

https://doi.org/10.1007/s12275-011-1213-z

https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git

Path: workflows/rna-selector.cwl

Branch/Commit ID: f993cad

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

Path: tests/record-output-wf.cwl

Branch/Commit ID: master