Nextflow Registry | nf-core/faqcs@0.0.0-6c4ed3a

nf-core/faqcs @ 0.0.0-6c4ed3a

Perform adapter and quality trimming on sequencing reads with reporting

trimming quality control fastq faqcs

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @mjcipriano @sateeshperi @hseabolt

Maintainers: @mjcipriano @sateeshperi @hseabolt

Perform adapter and quality trimming on sequencing reads with reporting

Add the following snippet to your workflow script to include this module.

include { FAQCS } from 'nf-core/faqcs'

MIT License

Process

`Name`	`FAQCS`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`reads` file	List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.

Output 8 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.log` file	fastq log file `*.log`

#2 debug tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`./debug` directory	trimming/qc files from --debug option `./debug`

#3 reads tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.trimmed.fastq.gz` file	The trimmed/modified fastq reads `*trimmed.fastq.gz`

#4 stats tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.stats.txt` file	trimming/qc text stats file `*.stats.txt`

#5 statspdf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*_qc_report.pdf` file	trimming/qc pdf report file `*_qc_report.pdf`

#6 versions

`versions.yml` file	File containing software versions `versions.yml`

#7 reads_fail tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.discard.fastq.gz` file	Reads that failed the preprocessing (Optional with --discard args setting) `*discard.fastq.gz`

#8 reads_unpaired tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.trimmed.unpaired.fastq.gz` file	Reads without matching mates in paired-end files (Optional) `*trimmed.unpaired.fastq.gz`

Tool	Description	Homepage
faqcs	FaQCs combines several features of currently available applications into a single, user-friendly process, and includes additional unique capabilities such as filtering the PhiX control sequences, conversion of FASTQ formats, and multi-threading. The original data and trimmed summaries are reported within a variety of graphics and reports, providing a simple way to do data quality control and assurance.	https://github.com/LANL-Bioinformatics/FaQCs

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:15:21 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Ffaqcs/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/faqcs/blobs/sha256:09205a6b7a65fbb8c3a9d201f57824b9c5b945ef5df4da51648841033f2815ff
Size	4.6 KB
Checksum	sha256:09205a6b7a65fbb8c3a9d201f57824b9c5b945ef5df4da51648841033f2815ff