Workflows

What is a Workflow?
743 Workflows visible to you, out of a total of 798

Pipeline to run and benchmark multiple sequence alignment tools.

Type: Nextflow

Creators: Luisa Santus, Jose Espinosa Carrasco

Submitter: WorkflowHub Bot

Work-in-progress

Workflow for microbial (meta-)genome annotation

Input is a (meta)genome sequence in fasta format.

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

Type: Common Workflow Language

Creators: Jasper Koehorst, Bart Nijsse

Submitter: Bart Nijsse

Work-in-progress

Workflow for converting (genome) annotation tool output into a GBOL RDF file (TTL/HDT) using SAPP

Current formats / tools:

  • EMBL format
  • InterProScan (JSON/TSV)
  • eggNOG-mapper (TSV)
  • KoFamScan (TSV)

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

SAPP (Semantic Annotation Platform with Provenance):
https://gitlab.com/sapp
https://academic.oup.com/bioinformatics/article/34/8/1401/4653704

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

Clinical Metaproteomics 4: Quantitation

Type: Galaxy

Creator: GalaxyP

Submitter: WorkflowHub Bot

Find and annotate variants in ampliconic SARS-CoV-2 Illumina sequencing data and classify samples with pangolin and nextclade

Type: Galaxy

Creators: Peter van Heusden, Peter van Heusden

Submitter: WorkflowHub Bot

This workflow takes a VCF dataset of variants produced by any of the *-variant-calling workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling and generates tabular lists of variants by Samples and by Variant, and an overview plot of variants and their allele-frequencies.

Type: Galaxy

Creators: Wolfgang Maier, Wolfgang Maier

Submitter: WorkflowHub Bot

COVID-19: variation analysis on ARTIC PE data

The workflow for Illumina-sequenced ampliconic data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming amplicon primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by primer-binding site mutations and, if possible, excludes reads derived from such ...

Assembly of bacterial paired-end short read data with generation of quality metrics and reports

Type: Galaxy

Creators: Abromics , Pierre Marin, Clea Siguret, abromics-consortium

Submitter: WorkflowHub Bot

Short paired-end read analysis to provide quality analysis, read cleaning and taxonomy assignation

Type: Galaxy

Creators: ABRomics , Pierre Marin, Clea Siguret, abromics-consortium

Submitter: WorkflowHub Bot

Stable

Current version of this workflow: https://workflowhub.eu/workflows/1109. Please use only with the new version. KNIME workflow to gather ChEMBL permeability data is availbale: https://workflowhub.eu/workflows/1169.

Type: KNIME

Creator: Kateřina Storchmannová

Submitter: Kateřina Storchmannová

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