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.wur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_metagenomics_assembly.cwl

Branch/Commit ID: master

https://github.com/cancerit/workflow-seq-import.git

Path: cwls/validate_interleaved_fq.cwl

Branch/Commit ID: 0.3.2

https://github.com/fgomez02/analysis-workflows.git

Path: definitions/subworkflows/phase_vcf.cwl

Branch/Commit ID: No_filters_detect_variants

run multiple rw stages sequentially using earlier step output as later stage input_bam

https://github.com/sentieon/sentieon-cwl.git

Path: stage/rw-flow.cwl

Branch/Commit ID: master

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

Path: tests/any-type-compat.cwl

Branch/Commit ID: main

abundace profiles from annotated files, for protein and/or rna

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

Path: CWL/Workflows/abundance.workflow.cwl

Branch/Commit ID: master

https://github.com/hpobio-lab/viral-analysis.git

Path: cwl/fastq2fasta/bam2fasta.cwl

Branch/Commit ID: master

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

Path: v1.0/v1.0/io-any-wf-1.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: annotator_sub_wf.cwl

Branch/Commit ID: 1.0.0

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

Path: definitions/pipelines/germline_exome.cwl

Branch/Commit ID: 6bfb64375e7ebb6eb40f463ede86d8deccdb9eff