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/genome/analysis-workflows.git

Path: definitions/pipelines/aml_trio_cle.cwl

Branch/Commit ID: master

BAM filtering

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/subworkflows/bam_filtering.cwl

Branch/Commit ID: 1.0.5

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

Path: setup/cwl/module-2.cwl

Branch/Commit ID: dev

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

Path: cwls/validate_interleaved_fq.cwl

Branch/Commit ID: 0.5.0_test

https://github.com/ICGC-TCGA-PanCancer/Seqware-BWA-Workflow.git

Path: checker-workflow-wrapping-workflow.cwl

Branch/Commit ID: 2.6.8_1.4

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/harmonization/alignment_bwa_mem_prod.cwl

Branch/Commit ID: master

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

Path: v1.0/v1.0/dynresreq-workflow-tooldefault.cwl

Branch/Commit ID: master

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

Path: pipeline.cwl

Branch/Commit ID: 20ea8da

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

Path: tests/record-in-secondaryFiles-missing-wf.cwl

Branch/Commit ID: master