Workflows

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70 Workflows visible to you, out of a total of 81
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

Work-in-progress

Workflow for (paired) read quality control, trimming and contamination filtering based on a given reference.

Will output a merged set of read pairs, when multiple datasets are used.

Steps:

  • FastQC (read quality control)

  • fastp (read quality trimming)

  • bbduk used (rrna filtering)

  • bbmap (contamination filter)

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

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.

alt text

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 ...

Stable

COnSensus Interaction Network InFErence Service

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

alt text

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 ...

Type: Common Workflow Language

Creators: Laura Rodriguez-Navas, José Mª Fernández

Submitter: Laura Rodriguez-Navas

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

Creators: None

Submitter: Yvan Le Bras

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