Description

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

Input

name:type
description
pattern

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.

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

name:type
description
pattern

filtered

meta:map

Groovy Map containing information on experiment. e.g. [ id:‘test’ ]

*.filtered.tsv:file

Filtered version of input matrix

*.filtered.tsv

tests

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

session_info

meta:map

Groovy Map containing information on experiment. e.g. [ id:‘test’ ]

R_sessionInfo.log:file

Log file containing R session information

*.log

versions

versions.yml:file

File containing software versions

versions.yml

Tools

matrixfilter

filter a matrix based on a minimum value and numbers of samples

https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/matrixfilter/main.nf
included in
differentialabundance
maintainer
Github user pinin4fjords
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