Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph Metagenomics workflow

Workflow for Metagenomics from raw reads to annotated bins. Steps: - workflow_quality.cwl: - FastQC (control) - fastp (quality trimming) - bbmap contamination filter - SPAdes (Assembly) - QUAST (Assembly quality report) - BBmap (Read mapping to assembly) - MetaBat2 (binning) - CheckM (bin completeness and contamination) - GTDB-Tk (bin taxonomic classification)

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

Path: cwl/workflows/workflow_metagenomics.cwl

Branch/Commit ID: 0dd868de067a386be8ec6b147df007e213c7275a
workflow graph secret_wf.cwl

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

Path: tests/wf/secret_wf.cwl

Branch/Commit ID: d5f7fa162611243f0c66dd3e933c16a4964a09ca
workflow graph Filter ChIP/ATAC peaks for Tag Density Profile or Motif Enrichment analyses

Filters ChIP/ATAC peaks with the neatest genes assigned for Tag Density Profile or Motif Enrichment analyses ============================================================================================================ Tool filters output from any ChIP/ATAC pipeline to create a file with regions of interest for Tag Density Profile or Motif Enrichment analyses. Peaks with duplicated coordinates are discarded.

https://github.com/datirium/workflows.git

Path: workflows/filter-peaks-for-heatmap.cwl

Branch/Commit ID: f3e44d3b0f198cf5245c49011124dc3b6c2b06fd
workflow graph blastp_wnode_naming

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

Path: task_types/tt_blastp_wnode_naming.cwl

Branch/Commit ID: f1eb0f4eaaf1661044f28d859f7e8d4302525ead
workflow graph lobSTR-workflow.cwl

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

Path: src/test/resources/cwl/lobstr-v1/lobSTR-workflow.cwl

Branch/Commit ID: 2e0114d3a1d9c0434e0334a21fa02da682d13d46
workflow graph Merge, annotate, and generate a TSV for SVs

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

Path: definitions/subworkflows/merge_svs.cwl

Branch/Commit ID: a08de598edc04f340fdbff76c9a92336a7702022
workflow graph Filter differentially expressed genes from DESeq for Tag Density Profile Analyses

Filters differentially expressed genes from DESeq for Tag Density Profile Analyses ================================================================================== Tool filters output from DESeq pipeline run for genes to create a file with regions of interest for Tag Density Profile Analyses.

https://github.com/datirium/workflows.git

Path: workflows/filter-deseq-for-heatmap.cwl

Branch/Commit ID: 9e3c3e65c19873cd1ed3cf7cc3b94ebc75ae0cc5
workflow graph beast-2step-workflow.cwl

https://github.com/GusEllerm/CWL_workflows.git

Path: workflows/BEAST_examples/beast-2step-workflow.cwl

Branch/Commit ID: 2c9b239c9a6278303c68357763bc9481a2ac1a3f
workflow graph Alignment without BQSR

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

Path: definitions/subworkflows/sequence_to_bqsr_nonhuman.cwl

Branch/Commit ID: a08de598edc04f340fdbff76c9a92336a7702022
workflow graph SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination

Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs.

https://github.com/datirium/workflows.git

Path: tools/soupx-subworkflow.cwl

Branch/Commit ID: 9e3c3e65c19873cd1ed3cf7cc3b94ebc75ae0cc5