runs a differential expression analysis with DESeq2
Input
name:type
description
pattern
meta{:bash}
: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{:bash}
:string
The column in the sample sheet that should be used to define groups for
comparison
reference{:bash}
:string
The value within the contrast_variable column of the sample sheet that
should be used to derive the reference samples
target{:bash}
:string
The value within the contrast_variable column of the sample sheet that
should be used to derive the target samples
formula{:bash}
:string
(Optional) R formula string used for modeling, e.g. ’~ treatment’.
comparison{:bash}
:string
(Optional, mandatory if formula is provided) Literal string for contrasts, e.g. ‘treatmenthND6’.
meta2{:bash}
:map
Groovy map containing study-wide metadata related to the sample sheet
and matrix
samplesheet{:bash}
:file
CSV or TSV format sample sheet with sample metadata
counts{:bash}
:file
Raw TSV or CSV format expression matrix as output from the nf-core
RNA-seq workflow
meta3{:bash}
:map
Meta map describing control genes, e.g. [ id: ‘ERCC’ ]
control_genes_file{:bash}
:file
Text file listing control genes, one per line
meta4{:bash}
:map
Groovy map containing study-wide metadata related to the transcript
lengths file
transcript_lengths_file{:bash}
:file
Optional file of transcript lengths, with the same sample columns as
counts. If supplied, lengths will be supplied to DESeq2 to correct for
differences in average transcript lengths across samples.
Output
name:type
description
pattern
results{:bash}
meta{:bash}
:map
Groovy Map containing contrast information, same as input meta
*.deseq2.results.tsv{:bash}
:file
TSV-format table of differential expression information as output by DESeq2
*.deseq2.results.tsv
dispersion_plot_png{:bash}
meta{:bash}
:map
Groovy Map containing contrast information, same as input meta
*.deseq2.dispersion.png{:bash}
:file
DESeq2 dispersion plot in PNG format
*.deseq2.dispersion.png
dispersion_plot_pdf{:bash}
meta{:bash}
:map
Groovy Map containing contrast information, same as input meta
*.deseq2.dispersion.pdf{:bash}
:file
DESeq2 dispersion plot in PDF format
*.deseq2.dispersion.pdf
rdata{:bash}
meta{:bash}
:map
Groovy Map containing contrast information, same as input meta
*.dds.rld.rds{:bash}
:file
Serialised DESeq2 object
*.dds.rld.rds
size_factors{:bash}
meta{:bash}
:map
Groovy Map containing contrast information, same as input meta
*.deseq2.sizefactors.tsv{:bash}
:file
TSV-format table containing DESeq2 size factors
*.deseq2.sizefactors.tsv
normalised_counts{:bash}
meta{:bash}
:map
Groovy Map containing contrast information, same as input meta
*.normalised_counts.tsv{:bash}
:file
TSV-format counts matrix, normalised to size factors
*.normalised_counts.tsv
rlog_counts{:bash}
meta{:bash}
:map
Groovy Map containing contrast information, same as input meta
*.rlog.tsv{:bash}
:file
Optional, TSV-format counts matrix, normalised to size factors, with
variance stabilisation applied via rlog().
*.rlog.tsv
vst_counts{:bash}
meta{:bash}
:map
Groovy Map containing contrast information, same as input meta
*.vst.tsv{:bash}
:file
Optional, TSV-format counts matrix, normalised to size factors, with
variance stabilisation applied via vst().
*.vst.tsv
model{:bash}
meta{:bash}
:map
Groovy Map containing contrast information, same as input meta
*.deseq2.model.txt{:bash}
:file
TXT-format DESeq2 model
*.deseq2.model.txt
session_info{:bash}
meta{:bash}
:map
Groovy Map containing contrast information, same as input meta
*.R_sessionInfo.log{:bash}
:file
Dump of R SessionInfo
*.R_sessionInfo.log
versions{:bash}
versions.yml{:bash}
:file
File containing software versions
versions.yml
Tools
deseq2
LGPL >=3
Differential gene expression analysis based on the negative binomial distribution
