Workflows

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831 Workflows visible to you, out of a total of 904
16S_biodiversity_BIOM
Stable

This is a Galaxy workflow that uses to convert the16S BIOM file to table and figures. It is part of the metaDEGalaxy workflow MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data.

Type: Galaxy

Creator: Mike Thang

Submitter: Mike Thang

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HI-FRIENDS HI data cube source finding and characterization
Stable

This repository contains the workflow used to find and characterize the HI sources in the data cube of the SKA Data Challenge 2. It was developed to process a simulated SKA data cube data cube, but can be adapted for clean HI data cubes from other radio observatories.

The workflow is managed and executed using snakemake workflow management system. It uses https://spectral-cube.readthedocs.io/en/latest/ based on ...

Type: Snakemake

Creators: None

Submitter: Javier Moldon

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ORSON: workflow for prOteome and tRanScriptome functiOnal aNnotation
Stable

ORSON combine state-of-the-art tools for annotation processes within a Nextflow pipeline: sequence similarity search (PLAST, BLAST or Diamond), functional annotation retrieval (BeeDeeM) and functional prediction (InterProScan). When required, BUSCO completness evaluation and eggNOG Orthogroup annotation can be activated. While ORSON results can be analyzed through the command-line, it also offers the possibility to be compatible with BlastViewer or Blast2GO graphical tools.

Type: Nextflow

Creators: Cyril Noel, Alexandre Cormier, Patrick Durand, Laura Leroi, Pierre Cuzin

Submitter: Patrick Durand

DOI: 10.48546/workflowhub.workflow.136.1

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1: Plant virus detection with kraken2 (SE)
Stable

Metagenomic dataset taxonomic classification using kraken2

Type: Galaxy

Creators: None

Submitter: johan Rollin

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1: Plant virus detection with kraken2 (PE)
Stable

Metagenomic dataset taxonomic classification using kraken2

Type: Galaxy

Creators: None

Submitter: johan Rollin

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Spliced RNAseq workflow
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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NonSpliced RNAseq workflow
Work-in-progress

Workflow for NonSpliced RNAseq data with multiple aligners.

Steps:

  • workflow_quality.cwl:
  • FastQC (control)
  • fastp (trimming)
  • bowtie2 (read mapping)
  • sam_to_sorted-bam
  • featurecounts (transcript read counts)
  • kallisto (transcript [pseudo]counts)

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

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NGTax
Stable

Amplicon analysis workflow using NG-Tax

Steps:

  • Quality control on the reads
  • Execute NGTax for ASV detection and classification

For more information about NG-Tax 2.0 have a look at https://doi.org/10.3389/fgene.2019.01366

Type: Common Workflow Language

Creators: Jasper Koehorst, Bart Nijsse, Jesse van Dam, Peter Schaap,

Submitter: Jasper Koehorst

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SPARQL query (in a file) on graph database
Work-in-progress

A workflow querying on an endpoint of a graph database by a file containing a SPARQL query.

Type: Common Workflow Language

Creators: None

Submitter: Qinqin Long

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Compute daily and monthly mean from meteorological station measurements
Stable

This workflow is used to process timeseries from meteorological stations in Finland but can be applied to any timeseries according it follows the same format.

Take a temperature timeseries from any meteorological station. Input format is csv and it must be standardized with 6 columns:

  1. Year (ex: 2021)
  2. month (ex: 1)
  3. day (ex: 15)
  4. Time (ex: 16:56)
  5. Time zone (such as UTC)
  6. Air temperature (degC)

Type: Galaxy

Creators: None

Submitter: Anne Fouilloux

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