Nextflow Registry | nf-core/mageck/test@0.0.0-0c7146d

nf-core/mageck/test @ 0.0.0-0c7146d

Mageck test performs a robust ranking aggregation (RRA) to identify positively or negatively selected genes in functional genomics screens.

sort rra CRISPR

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @LaurenceKuhl

Maintainers: @LaurenceKuhl

Mageck test performs a robust ranking aggregation (RRA) to identify positively or negatively selected genes in functional genomics screens.

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

include { MAGECK_TEST } from 'nf-core/mageck/test'

MIT License

Process

`Name`	`MAGECK_TEST`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`count_table` file	Count table file. Each line in the table should include sgRNA name (1st column), target gene (2nd column) and read counts in each sample. `*.{txt,tsv}`

Output 4 channels

#1 r_script tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.R` file	R script allowing to output plots from main hit genes `*.R`

#2 versions

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

#3 gene_summary tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.gene_summary.txt` file	Gene summary file describing the fitness score and associated p-values. `*.{gene_summary.txt}`

#4 sgrna_summary tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.sgrna_summary.txt` file	sgRNA summary file describing the sgRNA and associated gene `*.{sgrna_summary.txt}`

Tool	Description	Homepage
mageck	MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data.	https://sourceforge.net/p/mageck/wiki/Home/#mle

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:53:09 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fmageck%2Ftest/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/mageck/test/blobs/sha256:fd329e32d7f1951415f3b2aa9dc19c079aed73097feae8cb96f7a48f2d241920
Size	3.0 KB
Checksum	sha256:fd329e32d7f1951415f3b2aa9dc19c079aed73097feae8cb96f7a48f2d241920
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:53:09 (UTC)		1	3.0 KB	-