Workflows

What is a Workflow?
13 Workflows visible to you, out of a total of 13
Work-in-progress

Workflow (hybrid) metagenomic assembly and binning + GEMs

Accepts both Illumina and Long reads (ONT/PacBio)

Workflow binnning https://workflowhub.eu/workflows/64?version=11 (optional)

  • Metabat2/MaxBin2/SemiBin
  • DAS Tool
  • CheckM ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

Work-in-progress

Workflow for LongRead Quality Control and Filtering

  • NanoPlot (read quality control) before and after filtering
  • Filtlong (read trimming)
  • Kraken2 taxonomic read classification before and after filtering
  • Minimap2 read filtering based on given references

Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default

All tool CWL files and other workflows can be found here: https://gitlab.com/m-unlock/cwl/workflows

**How to setup and use an UNLOCK ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst, Germán Royval

Submitter: Bart Nijsse

Stable

Workflow for Illumina Quality Control and Filtering

Multiple paired datasets will be merged into single paired dataset.

Summary:

  • FastQC on raw data files
  • fastp for read quality trimming
  • BBduk for phiX and (optional) rRNA filtering
  • Kraken2 for taxonomic classification of reads (optional)
  • BBmap for (contamination) filtering using given references (optional)
  • FastQC on filtered (merged) data

Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

- Deprecated -

See our updated hybrid assembly workflow: https://workflowhub.eu/workflows/367

And other workflows: https://workflowhub.eu/projects/16#workflows

Workflow for sequencing with ONT Nanopore data, from basecalled reads to (meta)assembly and binning

  • Workflow Nanopore Quality
  • Kraken2 taxonomic classification of FASTQ reads
  • Flye (de-novo assembly)
  • Medaka (assembly polishing)
  • metaQUAST (assembly quality reports)

When Illumina reads are provided:

  • Workflow ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst, Germán Royval

Submitter: Jasper Koehorst

Work-in-progress

Workflow for Metagenomics from bins to metabolic models (GEMs)

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

All tool CWL files and other workflows can be found here: Tools: https://gitlab.com/m-unlock/cwl Workflows: https://gitlab.com/m-unlock/cwl/workflows

**How ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

Work-in-progress

Workflow for Metagenomics binning from assembly

Minimal inputs are: Identifier, assembly (fasta) and a associated sorted BAM file

Summary

  • MetaBAT2 (binning)
  • MaxBin2 (binning)
  • SemiBin (binning)
  • DAS Tool (bin merging)
  • EukRep (eukaryotic classification)
  • CheckM (bin completeness and contamination)
  • BUSCO (bin completeness)
  • GTDB-Tk (bin taxonomic classification)

Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default

**All tool CWL ...

Type: Common Workflow Language

Creators: Jasper Koehorst, Bart Nijsse

Submitter: Jasper Koehorst

Workflow Kallisto RNAseq

(pseudoalignment on transcripts)

All tool CWL files and other workflows can be found here:
Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl
Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows

How to setup and use an UNLOCK workflow:
https://m-unlock.gitlab.io/docs/setup/setup.html

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

- deprecated -

Workflow for sequencing with ONT Nanopore, from basecalling to assembly.

  • Guppy (basecalling of raw reads)
  • MinIONQC (quality check)
  • FASTQ merging from multi into one file
  • Kraken2 (taxonomic classification)
  • Krona (classification visualization)
  • Flye (de novo assembly)
  • Medaka (assembly polishing)
  • QUAST (assembly quality reports)

All tool CWL files and other workflows can be found here: Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl Workflows: ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst, Germán Royval

Submitter: Jasper Koehorst

Workflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2. 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
  • Picrust 2
  • Export module for ngtax

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Jasper Koehorst

DOI: 10.48546/workflowhub.workflow.154.2

Work-in-progress

Workflow for Spliced RNAseq data Steps:

  • workflow_quality.cwl:
  • FastQC (Read Quality Control)
  • fastp (Read Trimming)
  • STAR (Read mapping)
  • featurecounts (transcript read counts)
  • kallisto (transcript [pseudo]counts)

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

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