Nextflow Registry | nf-core/custom/matrixfilter@0.0.0-3fc6d40

nf-core/custom/matrixfilter @ 0.0.0-3fc6d40

filter a matrix based on a minimum value and numbers of samples that must pass.

matrix filter abundance na

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @pinin4fjords

Maintainers: @pinin4fjords

filter a matrix based on a minimum value and numbers of samples that must pass.

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

include { CUSTOM_MATRIXFILTER } from 'nf-core/custom/matrixfilter'

MIT License

Process

`Name`	`CUSTOM_MATRIXFILTER`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing information on matrix to be filtered, at a minimum an id. e.g. [ id:'test' ]
`abundance` file	Raw TSV or CSV format abundance matrix with features (e.g. genes) by row and observations (e.g. samples) by column. All rownames from the sample sheet should be present in the columns.

#2 tuple

`samplesheet_meta` map	Where samplesheet is provided, aroovy Map containing information on sample sheet, at a minimum an id. e.g. [ id:'test' ]
`samplesheet` file	Optional CSV or TSV format sample sheet with sample metadata. If provided this is used to infer minimum passing samples from group sizes present (see grouping_variable), but also to validate matrix columns. If not provided, all numeric columns are selected.

Output 5 channels

#1 tests tuple

`meta` map	Groovy Map containing information on experiment. e.g. [ id:'test' ]
`*.tests.tsv` file	Boolean matrix with pass/ fail status for each test on each feature `*.tests.tsv`

#2 filtered tuple

`meta` map	Groovy Map containing information on experiment. e.g. [ id:'test' ]
`*.filtered.tsv` file	Filtered version of input matrix `*.filtered.tsv`

#3 versions

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

#4 thresholds tuple

`meta` map	Groovy Map containing information on experiment. e.g. [ id:'test' ]
`*.thresholds.tsv` file	Table of filtering thresholds applied in matrix filtering `*.thresholds.tsv`

#5 session_info tuple

`meta` map	Groovy Map containing information on experiment. e.g. [ id:'test' ]
`*R_sessionInfo.log` file	Log file containing R session information `*.log`

Tool	Description	Homepage
matrixfilter	filter a matrix based on a minimum value and numbers of samples	n/a

Version	0.0.0-3fc6d40
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	22 Apr 2026 15:08:31 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fcustom%2Fmatrixfilter/0.0.0-3fc6d40/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/custom/matrixfilter/blobs/sha256:b76caf74388c27ada9aa27961e4185dcb0c39b47fe96a8f6e3d7729e4faab472
Size	7.1 KB
Checksum	sha256:b76caf74388c27ada9aa27961e4185dcb0c39b47fe96a8f6e3d7729e4faab472
Downloads	3

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:12:12 (UTC)	3	7.0 KB
0.0.0-3fc6d40	22 Apr 2026 15:08:31 (UTC)	3	7.1 KB
0.0.0-0c7146d	08 Apr 2026 18:55:18 (UTC)	3	7.0 KB