Workflows

What is a Workflow?
301 Workflows visible to you, out of a total of 324
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.

Stable

Metagenomic dataset taxonomic classification using kraken2

Type: Galaxy

Creators: None

Submitter: johan Rollin

Stable

Metagenomic dataset taxonomic classification using kraken2

Type: Galaxy

Creators: None

Submitter: johan Rollin

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

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

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

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

Stable

COnSensus Interaction Network InFErence Service

Inference framework for reconstructing networks using a consensus approach between multiple methods and data sources.

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Reference

[Manica, Matteo, Charlotte, Bunne, Roland, Mathis, Joris, Cadow, Mehmet Eren, Ahsen, Gustavo A, Stolovitzky, and María Rodríguez, Martínez. "COSIFER: a python package for the consensus inference of molecular ...

Work-in-progress

Workflow to take DataOne data packages (raw datasets + metadata written in Ecological Metadata Standard) as input and create a DwC occurence.csv file almost ready to put in a Dawrin core Archive using eml-annotations at the attribute level

Type: Galaxy

Creator: Yvan Le Bras

Submitter: Yvan Le Bras

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