Nextflow Registry | nf-core/fast2q@0.0.0-e2d3f0d

nf-core/fast2q @ 0.0.0-e2d3f0d

A program that counts sequence occurrences in FASTQ files.

CRISPRi FASTQ genomics

Latest version: 0.0.0-e2d3f0d

Total downloads: 2

Source: nf-core/modules

Authors: @afombravo

Maintainers: @afombravo

A program that counts sequence occurrences in FASTQ files.

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

include { FAST2Q } from 'nf-core/fast2q'

MIT License

Process

`Name`	`FAST2Q`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing output name. e.g. [ id:'test']
`fastq` directory	Folder with FASTQ file(s). 2FAST2Q automatically picks up all the FASTQ files inside the provided folder. `*.{fastq,gz}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'library_name', multiple_features_per_read:false ]
`library` file	.csv library file following the ´Feature_name,sequence´ or ´Feature_name,sequence1:sequence2´ format. See 2FAST2Q instructions for more information. `*.csv`

Output 6 channels

#1 stats tuple

`meta` map	Groovy Map containing output name. e.g. [ id:'test' ]
`${prefix}_stats.csv` file	File containing all the relevant statistics such as quality passing reads, aligned reads, total reads, and sample run times.

#2 reads_plot tuple

`meta` map	Groovy Map containing output name. e.g. [ id:'test' ]
`${prefix}_reads_plot.png` file	Bar plot with the distribution of reads, in absolute numbers, binned to the different quality metrics indicated in the statistics.csv

#3 count_matrix tuple

`meta` map	Groovy Map containing output name. e.g. [ id:'test' ]
`${prefix}.csv` file	Count matrix csv file

#4 versions_fast2q tuple

`${task.process}` string	The name of the process
`fast2q` string	The name of the tool
`2fast2q -v \| sed -n "s/Version: //p"` eval	The expression to obtain the version of the tool

#5 distribution_plot tuple

`meta` map	Groovy Map containing output name. e.g. [ id:'test' ]
`${prefix}_distribution_plot.png` file	Violin plot of the distribution of reads per feature across all samples.

#6 reads_plot_percentage tuple

`meta` map	Groovy Map containing output name. e.g. [ id:'test' ]
`${prefix}_reads_plot_percentage.png` file	Bar plot with the distribution of reads, in percentage, binned to the different quality metrics indicated in the statistics.csv

Tool	Description	Homepage
2FAST2Q	2FAST2Q is ideal for CRISPRi-Seq, and for extracting and counting any kind of information from reads in the fastq format, such as barcodes in Bar-seq experiments. 2FAST2Q can work with sequence mismatches, Phred-score, and be used to find and extract unknown sequences delimited by known sequences. 2FAST2Q can extract multiple features per read using either fixed positions or delimiting search sequences.	https://github.com/afombravo/2FAST2Q

Version	0.0.0-e2d3f0d
Commit ID	e2d3f0ddf4a74a4a9031f3caea2e9deaec5a440b
Release Date	28 Apr 2026 21:15:28 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Ffast2q/0.0.0-e2d3f0d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/fast2q/blobs/sha256:e0f30e31c9f7743c245201cafbf7de750463e4bcdff745ae3278963f1a61f7ae
Size	3.5 KB
Checksum	sha256:e0f30e31c9f7743c245201cafbf7de750463e4bcdff745ae3278963f1a61f7ae
Downloads	1

Version	Date	Status	Downloads	Size	Diff