runs a differential expression analysis with Limma
Input
name:type
description
pattern
meta
:map
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’.
contrast_variable
:string
(Optional, required if reference and target are used) The column in the sample sheet that should be used to define groups for
comparison
reference
:string
(Optional, required if contrast_variable and target are used) The value within the contrast_variable column of the sample sheet that
should be used to derive the reference samples
target
:string
(Optional, required if contrast_variable and reference are used) The value within the contrast_variable column of the sample sheet that
should be used to derive the target samples
formula
:string
(Optional, requires comparison if used) R formula string used for modeling, e.g. ’~ treatment’.
comparison
:string
(Optional, mandatory if formula is used) Literal string passed to limma::makeContrasts, e.g. ‘treatmentmCherry’.
meta2
:map
Groovy map containing study-wide metadata related to the sample sheet
and matrix
samplesheet
:file
Sample sheet file
intensities
:file
Raw TSV or CSV format expression matrix with probes by row and samples
by column
Output
name:type
description
pattern
results
meta
:map
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’.
*.limma.results.tsv
:file
TSV-format table of differential expression information as output by Limma
*.limma.results.tsv
md_plot
meta
:map
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’.
*.limma.mean_difference.png
:file
Limma mean difference plot
*.mean_difference.png
rdata
meta
:map
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’.
*.MArrayLM.limma.rds
:file
Serialised MArrayLM object
*.MArrayLM.limma.rds
model
meta
:map
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’.
*.limma.model.txt
:file
TXT-format limma model
*.limma.model.tsv
session_info
meta
:map
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’.
*.R_sessionInfo.log
:file
dump of R SessionInfo
*.log
normalised_counts
meta
:map
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’.
*.normalised_counts.tsv
:file
normalised TSV format expression matrix with probes by row and samples by column
