Workflows

What is a Workflow?
558 Workflows visible to you, out of a total of 602
Nanopore Assembly Workflow - Deprecated -

- 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

TF-Prioritizer
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

Reconstructing raw tomography data

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

DOI: 10.48546/workflowhub.workflow.432.1

cutandrun/main

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

hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler

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

TronFlow BAM preprocessing pipeline
Stable

TronFlow BAM preprocessing pipeline

GitHub tag (latest SemVer) Automated tests DOI ...

Type: Nextflow

Creators: None

Submitter: Pablo Riesgo Ferreiro

TronFlow alignment pipeline
Stable

TronFlow alignment pipeline

GitHub tag (latest SemVer) Run tests DOI ...

Type: Nextflow

Creators: None

Submitter: Pablo Riesgo Ferreiro

CoVigator pipeline: variant detection pipeline for Sars-CoV-2 (and other viruses...)
Stable

CoVigator logo

CoVigator pipeline: variant detection pipeline for Sars-CoV-2

DOI Run tests [![Powered by ...

Type: Nextflow

Creators: Pablo Riesgo Ferreiro, Thomas Bukur, Patrick Sorn

Submitter: Pablo Riesgo Ferreiro

atacseq/main

This workflow take as input a collection of paired fastq. It will remove bad quality and adapters with cutadapt. Map with Bowtie2 end-to-end. Will remove reads on MT and unconcordant pairs and pairs with mapping quality below 30 and PCR duplicates. Will compute the pile-up on 5' +- 100bp. Will call peaks and count the number of reads falling in the 1kb region centered on the summit. Will plot the number of reads for each fragment length.

Type: Galaxy

Creators: Lucille Delisle, Lucille Delisle

Submitter: WorkflowHub Bot

rnaseq-sr/main

This workflow takes as input a list of single-read fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously. The counts are reprocess to be similar to HTSeq-count output. FPKM are computed with cufflinks. Coverage (per million mapped reads) are computed with bedtools on uniquely mapped reads.

Type: Galaxy

Creators: Lucille Delisle, Lucille Delisle

Submitter: WorkflowHub Bot

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