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

This is a subworkflow of the main oxog_varbam_annotat_wf workflow - this is not meant to be run as a stand-alone workflow!

https://github.com/ICGC-TCGA-PanCancer/OxoG-Dockstore-Tools.git

Path: oxog_sub_wf.cwl

Branch/Commit ID: develop

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

Path: tools/rRNA_selection.cwl

Branch/Commit ID: master

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

Path: v1.0/v1.0/io-file-default-wf.cwl

Branch/Commit ID: master

https://github.com/mskcc/roslin-variant.git

Path: setup/cwl/module-5.cwl

Branch/Commit ID: 2.4.x

This is a subworkflow of the main oxog_varbam_annotat_wf workflow - this is not meant to be run as a stand-alone workflow!

https://github.com/svonworl/oxog-dockstore-tools.git

Path: oxog_sub_wf.cwl

Branch/Commit ID: master

This workflow aligns the fastq files using STAR for no spliced genomes

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

Path: workflows/Alignments/star-alignment-nosplice.cwl

Branch/Commit ID: master

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

Path: v1.0/v1.0/count-lines6-wf.cwl

Branch/Commit ID: master

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

Path: tests/count-lines16-wf.cwl

Branch/Commit ID: master

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

Path: v1.0/v1.0/count-lines11-extra-step-wf-noET.cwl

Branch/Commit ID: master