Explore Workflows

Workflow for Metagenomics from raw reads to annotated bins. Steps: - workflow_illumina_quality.cwl: - FastQC (control) - fastp (quality trimming) - kraken2 (taxonomy) - bbmap contamination filter - SPAdes (Assembly) - QUAST (Assembly quality report) - BBmap (Read mapping to assembly) - Contig binning (OPTIONAL)

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

Path: cwl/workflows/workflow_metagenomics_assembly.cwl

Branch/Commit ID: master

STARR-seq 03 mapping - reads: PE

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

Path: v1.0/STARR-seq_pipeline/03-map-pe-umis.cwl

Branch/Commit ID: 487af88ef0b971f76ecd1a215639bb47e3ee94e1

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

Path: workflows/functional_analysis.cwl

Branch/Commit ID: 5dc7c5c

https://github.com/lukasheinrich/cwltests.git

Path: cwl/workflow_data.cwl

Branch/Commit ID: master

https://github.com/tmooney/cancer-genomics-workflow.git

Path: definitions/subworkflows/docm_germline.cwl

Branch/Commit ID: downsample_and_recall

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

Path: tools/rRNA_selection.cwl

Branch/Commit ID: master

Sub workflow used in the Animal Genome Assembly pipeline by Kazuharu Arakawa (@gaou_ak), CWLized by Tazro Ohta (@inutano)

https://github.com/pitagora-network/DAT2-cwl.git

Path: workflow/animal-genome-assembly/hybrid_error_correction.cwl

Branch/Commit ID: main

todo

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

Path: CWL/Workflows/relabel-and-merge.cwl

Branch/Commit ID: wilke/20180622

https://github.com/inab/Wetlab2Variations.git

Path: cwl-workflows/demonstrator/workflow.cwl

Branch/Commit ID: master

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

Path: bacterial_ncrna/wf_gcmsearch.cwl

Branch/Commit ID: dev