modules/deseq2_differential

Groovy Map containing contrast information. This can be used at the
workflow level to pass optional parameters to the module, e.g.
[ id:‘contrast1’, blocking:‘patient’ ] passed in as ext.args like:
‘—blocking_variable $meta.blocking’.

The column in the sample sheet that should be used to define groups for
comparison

The value within the contrast_variable column of the sample sheet that
should be used to derive the reference samples

The value within the contrast_variable column of the sample sheet that
should be used to derive the target samples

Groovy map containing study-wide metadata related to the sample sheet
and matrix

CSV or TSV format sample sheet with sample metadata

Raw TSV or CSV format expression matrix as output from the nf-core
RNA-seq workflow

Text file listing control genes, one per line

Meta map describing control genes, e.g. [ id: ‘ERCC’ ]

Specify if any supplied control genes should just be stripped to
prevent bias in conventional normalisation (default), or used to
generate the size factors (supplied via task.ext.args like
‘—sizefactors_from_controls TRUE’).