ERGA DataQC Illumina v2309 (WF0)
Version 1

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Run on usegalaxy.eu

Workflow Type: Galaxy

Stable

The workflow takes a paired-reads collection (like illumina WGS or HiC), 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.

SEEK ID: https://workflowhub.eu/workflows/601?version=1

DOI: 10.48546/workflowhub.workflow.601.1

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