Explore Workflows

Allele specific RNA-Seq (using vcf) single-read workflow

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

Path: workflows/allele-vcf-rnaseq-se.cwl

Branch/Commit ID: 3ceeb2e90f49579369b2e10485908516348381a9

**Workflow (hybrid) metagenomic assembly and binning **<br> - Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1 - FastQC (control) - fastp (quality trimming) - kraken2 (taxonomy) - bbmap contamination filter - Kraken2 taxonomic classification of FASTQ reads - SPAdes/Flye (Assembly) - QUAST (Assembly quality report) (optional) - Workflow binnning https://workflowhub.eu/workflows/64?version=11 - Metabat2/MaxBin2/SemiBin - DAS Tool - CheckM - BUSCO - GTDB-Tk (optional) - Workflow Genome-scale metabolic models https://workflowhub.eu/workflows/372 - CarveMe (GEM generation) - MEMOTE (GEM test suite) - SMETANA (Species METabolic interaction ANAlysis) Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default<br><br> **All tool CWL files and other workflows can be found here:**<br> Tools: https://gitlab.com/m-unlock/cwl<br> Workflows: https://gitlab.com/m-unlock/cwl/workflows<br> **How to setup and use an UNLOCK workflow:**<br> https://m-unlock.gitlab.io/docs/setup/setup.html<br>

https://gitlab.com/m-unlock/cwl.git

Path: cwl/workflows/workflow_metagenomics_assembly.cwl

Branch/Commit ID: 50aaa5a89d0cd01c80d55fb68dd72708d3796503

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/scatter-wf4.cwl

Branch/Commit ID: 5f27e234b4ca88ed1280dedf9e3391a01de12912

Packed ID: main

This workflow will run OxoG, variantbam, and annotate. Run this as `dockstore --script --debug workflow launch --descriptor cwl --local-entry --entry ./oxog_varbam_annotate_wf.cwl --json oxog_varbam_annotat_wf.input.json `

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

Path: oxog_varbam_annotate_wf.cwl

Branch/Commit ID: b38a8a4785746b8267913ea5389e21ae6dc921a3

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: annotator_sub_wf.cwl

Branch/Commit ID: b38a8a4785746b8267913ea5389e21ae6dc921a3

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: minibam_sub_wf.cwl

Branch/Commit ID: b38a8a4785746b8267913ea5389e21ae6dc921a3

Workflow for quality assessment of paired reads and classification using NGTax 2.0. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps: - FastQC (read quality control) - NGTax 2.0 - Export module

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

Path: cwl/workflows/workflow_ngtax.cwl

Branch/Commit ID: b9097b82e6ab6f2c9496013ce4dd6877092956a0

Workflow for Metagenomics from bins to metabolic model.<br> Summary - Prodigal gene prediction - CarveMe genome scale metabolic model reconstruction - MEMOTE for metabolic model testing - SMETANA Species METabolic interaction ANAlysis Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default<br><br> **All tool CWL files and other workflows can be found here:**<br> Tools: https://gitlab.com/m-unlock/cwl<br> Workflows: https://gitlab.com/m-unlock/cwl/workflows<br> **How to setup and use an UNLOCK workflow:**<br> https://m-unlock.gitlab.io/docs/setup/setup.html<br>

https://gitlab.com/m-unlock/cwl.git

Path: cwl/workflows/workflow_metagenomics_GEM.cwl

Branch/Commit ID: 50aaa5a89d0cd01c80d55fb68dd72708d3796503

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

Path: structuralvariants/cwl/workflow.cwl

Branch/Commit ID: 94bcf49c6f22055a359336d2e593f8289f1c5e48

This workflow detect and remove contamination from a DNA fasta file

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

Path: workflows/Contamination/contaminant-cleanup.cwl

Branch/Commit ID: e1c19e64f6fc210f65472ee227786d33c9b4909a