Description

Make a GSEA class file (.cls) from tabular inputs

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing metadata including an id, the sample sheet column
used to define groups, and optionally a separator to override defaults e.g. [
id:‘test’, variable:‘treatment’, separator:’,’ ]. The way these values are
passed to the associated module parameters is then defined via an ext.args
specification for the process from the workflow, like: ext.args = { [
“separator”: “\t”, “variable”: “$meta.variable” ] } (‘variable’ is
compulsory here).

samples (file)

Tabular (e.g. TSV/CSV) samples file with sample IDs by row and variables by column.

*.{csv,tsv}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing metadata e.g. [ id:‘test’, variable:‘treatment’,
separator:’,’ ]

cls (file)

A categorical class format file (.cls) as defined by the Broad
documentation at
https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats

versions (file)

File containing software versions

versions.yml