Workflows

What is a Workflow?
Created At
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Updated At
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292 Workflows visible to you, out of a total of 305

- 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

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

Work-in-progress

Workflow for LongRead Quality Control and Filtering

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

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: ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst, Germán Royval

Submitter: Bart Nijsse

Work-in-progress

Workflow (hybrid) metagenomic assembly and binning + GEMs

Accepts both Illumina and Nanopore

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

  • Metabat2/MaxBin2/SemiBin
  • DAS Tool
  • CheckM
  • BUSCO
  • GTDB-Tk ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

Work-in-progress

1. About TF-Prioritizer

This pipeline gives you a full analysis of nfcore chromatine accessibility peak data (ChIP-Seq, ATAC-Seq or DNAse-Seq) and nfcore RNA-seq count data. It performs DESeq2, TEPIC and DYNAMITE including all preprocessing and postprocessing steps necessary to transform the data. It also gives you plots for deep analysis of the data. The general workflow is sketched in the images below:

Graphical abstract:

Graphical abstrat ...

Type: Unrecognized workflow type

Creators: None

Submitter: Nico Trummer

Snakemake workflow: Reconstructing raw tomography data

A Snakemake worfklow for tomographically reconstructing raw data using tomopy.

Installation

First download this repo and navigate to it

git clone https://codebase.helmholtz.cloud/gernha62/reconstructing-raw-tomography-data.git 
cd /path/to/repo 

(Optional) Download the example folder with:

wget -m -np https://doi2.psi.ch/datasets/das/work/p15/p15869/compression/MI04_02/tif
...

Type: Snakemake

Creator: Felicita Gernhardt

Submitter: Felicita Gernhardt

Work-in-progress

We present an R script that describes the workflow for analysing honey bee (Apis mellifera) wing shape. It is based on a large dataset of wing images and landmark coordinates available at Zenodo: https://doi.org/10.5281/zenodo.7244070. The dataset can be used as a reference for the identification of unknown samples. As unknown samples, we used data from Nawrocka et al. (2018), available at Zenodo: https://doi.org/10.5281/zenodo.7567336. Among others, the script can be used to identify the geographic ...

Type: R markdown

Creators: None

Submitter: Adam Tofilski

This workflow take as input a collection of paired fastq. Remove adapters with cutadapt, map pairs with bowtie2 allowing dovetail. Keep MAPQ30 and concordant pairs. BAM to BED. MACS2 with "ATAC" parameters.

Type: Galaxy

Creators: Lucille Delisle, Lucille Delisle

Submitter: WorkflowHub Bot

This workflow take as input a collection of paired fastq. It uses HiCUP to go from fastq to validPair file. The pairs are filtered for MAPQ and sorted by cooler to generate a tabix dataset. Cooler is used to generate a balanced cool file to the desired resolution.

Type: Galaxy

Creator: Lucille Delisle

Submitter: WorkflowHub Bot

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