Nextflow Registry | nf-core/fast2q@0.0.0-3fc6d40

nf-core/fast2q @ 0.0.0-3fc6d40

A program that counts sequence occurrences in FASTQ files.

CRISPRi FASTQ genomics

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

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 versions

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

#3 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

#4 count_matrix tuple

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

#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	0.0.0-3fc6d40
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	22 Apr 2026 15:11:16 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Ffast2q/0.0.0-3fc6d40/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/fast2q/blobs/sha256:118211cc6a1ca9b8ccd09b627134107028424ce2d5f8004492ae54ac7f445674
Size	3.6 KB
Checksum	sha256:118211cc6a1ca9b8ccd09b627134107028424ce2d5f8004492ae54ac7f445674
Downloads	4

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:15:23 (UTC)		3	3.6 KB
0.0.0-3fc6d40	22 Apr 2026 15:11:16 (UTC)		4	3.6 KB