ERGA DataQC Illumina v2309 (WF0)
Version 1

Workflow Type: Galaxy
Stable

The workflow takes a paired-reads collection, runs FastQC and SeqKit, trims with Fastp, and creates a MultiQC report. The main outputs are a paired collection of trimmed reads, a report with raw and trimmed reads stats, and a table with raw reads stats.

Inputs

ID Name Description Type
Raw illumina collection #main/Raw illumina collection n/a
  • array containing
    • File

Steps

ID Name Description
1 FastQC Illumina Raw toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
2 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0
3 SeqKit Illumina Raw toolshed.g2.bx.psu.edu/repos/iuc/seqkit_stats/seqkit_stats/2.3.1+galaxy1
4 Flatten collection __FLATTEN__
5 Flatten collection __FLATTEN__
6 MultiQC Illumina toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
7 Seqkit Illumina toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0

Outputs

ID Name Description Type
_anonymous_output_1 #main/_anonymous_output_1 n/a
  • File
_anonymous_output_2 #main/_anonymous_output_2 n/a
  • File
_anonymous_output_3 #main/_anonymous_output_3 n/a
  • File
_anonymous_output_4 #main/_anonymous_output_4 n/a
  • File

Version History

Version 1 (earliest) Created 6th Oct 2023 at 14:03 by Diego De Panis

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Frozen Version-1 5d1c4c7
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ERGA

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Views: 938

Created: 6th Oct 2023 at 14:03

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