short-read-qc-trimming/main
v0.3 (latest)

v0.3 (latest)

v0.2

v0.1 (earliest)

Workflow Type: Galaxy

This workflow performs quality control and trimming on paired-end Illumina fastq(.gz) files using fastp and aggregates the quality control reports with MultiQC

SEEK ID: https://workflowhub.eu/workflows/2025?version=3

Inputs

ID	Name	Description	Type
Adapter to remove on forward reads	#main/Adapter to remove on forward reads	Sequence of the adapter to remove from forward reads using fastp	string
Adapter to remove on reverse reads	#main/Adapter to remove on reverse reads	Sequence of the adapter to remove from reverse reads using fastp	string
Minimal read length	#main/Minimal read length	Reads shorter than this value will be discarded	int
Qualified quality score	#main/Qualified quality score	The quality value that a base is qualified. Default 15 means a quality score >=Q15 is qualified.	int
Raw reads	#main/Raw reads	Raw reads as paired-end collection	array containing File

Steps

ID	Name	Description
5	fastp	Quality control and trimming of the raw reads toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.1.0+galaxy0
6	MultiQC	Aggregation of the quality controls for all samples toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0

Outputs

ID	Name	Description	Type
MultiQC HTML report	#main/MultiQC HTML report	n/a	File
fastp JSON report	#main/fastp JSON report	n/a	File
fastp trimmed reads	#main/fastp trimmed reads	n/a	File

Version History

v0.3 (latest) Created 20th Feb 2026 at 03:02 by WorkflowHub Bot

Updated to v0.3

Frozen v0.3 3f17d6b

v0.2 Created 9th Dec 2025 at 03:02 by WorkflowHub Bot

Updated to v0.2

Frozen v0.2 30a7685

v0.1 (earliest) Created 4th Dec 2025 at 03:02 by WorkflowHub Bot

Updated to v0.1

Frozen v0.1 e19d684

Creators and Submitter

Creators

Submitter

WorkflowHub Bot

License

MIT License (MIT)

Activity

Views: 1255 Downloads: 264 Runs: 2

Created: 4th Dec 2025 at 03:02

short-read-qc-trimming/main v0.3 (latest) v0.3 (latest) v0.2 v0.1 (earliest)