Workflows

What is a Workflow?
1321 Workflows visible to you, out of a total of 1412

GitHub Actions CI Status GitHub Actions Linting StatusAWS CInf-test ...

Type: Nextflow

Creators: Daniel Straub, Alexander Peltzer

Submitter: WorkflowHub Bot

Evaluation of Pacbio Hifi Reads and genome profiling. Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.

Type: Galaxy

Creator: VGP, Galaxy

Submitter: WorkflowHub Bot

Decontamination (foreign contaminants and mitochondrial sequences) of a genome assembly after the final scaffolding step. Uses NCBI FCS GX to identify foreign contaminants and Blast to identify mitochondrial sequences. Part of the VGP Suite.

Type: Galaxy

Creators: Delphine Lariviere, Nadolina Brajuka

Submitter: WorkflowHub Bot

This workflow performs the scaffolding of a genome assembly using HiC data with YAHS. Can be used on any assembly with Hi-C data, and the assembly in the gfa format.

Type: Galaxy

Creator: VGP, Galaxy

Submitter: WorkflowHub Bot

Stable

The bioinformatic workflow presented here enables the analysis of RNA sequencing data obtained from human reproductive tissues in unexplained recurrent pregnancy loss (uRPL) research. This pipeline requires a sample sheet containing the sample information (example_input_data.csv) and gene expression matrices generated using the Salmon tool in the nf-core/rnaseq bioinformatics pipeline (example_count_data.csv). For more information on how to use the nf-core/rnaseq pipeline including the required ...

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite ...

Type: Nextflow

Creators: Jasmin Frangenberg, Anan Ibrahim, James A. Fellows Yates

Submitter: WorkflowHub Bot

Stable

WorkflowHub Knowledge Graph

A tool to generate a knowledge graph from a source of RO Crates. By default, this tool sources and generates an RDF graph of crates from WorkflowHub.

Docker build and push [![Python linting and ...

Work-in-progress

Workflow for Metagenomics binning from assembly.

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

Summary

  • MetaBAT2 (binning)
  • MaxBin2 (binning)
  • SemiBin2 (binning)
  • Binette (bin merging)
  • EukRep (eukaryotic classification)
  • CheckM2 (bin completeness and contamination)
  • BUSCO (bin completeness)
  • GTDB-Tk (bin taxonomic classification)
  • CoverM (bin abundances)

Including: Bin annotation (workflow: https://workflowhub.eu/workflows/1170):

  • Bakta

...

Type: Common Workflow Language

Creators: Jasper Koehorst, Bart Nijsse

Submitters: Jasper Koehorst, Bart Nijsse

Stable

GitHub last commit (branch) Status cwltool License Version [![Open in Dev ...

Type: Common Workflow Language

Creators: Ryo Mameda, Sora Yonezawa

Submitters: Sora Yonezawa, Ryo Mameda

DOI: 10.48546/workflowhub.workflow.1955.2

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