Description

runs a differential expression analysis with DESeq2

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)

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

reference (string)

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

target (string)

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

meta2 (map)

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

samplesheet (file)

CSV or TSV format sample sheet with sample metadata

counts (file)

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

meta3 (file)

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

control_genes_file (file)

Text file listing control genes, one per line

meta4 (map)

Groovy map containing study-wide metadata related to the transcript
lengths file

transcript_lengths_file (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 (file)

TSV-format table of differential expression information as output by DESeq2

deseq2.results.tsv

dispersion_plot (file)

DESeq2 dispersion plot

deseq2.dispersion.png

rdata (file)

Serialised DESeq2 object

dds.rld.rds

sizefactors (file)

Size factors

deseq2.sizefactors.tsv

normalised_counts (file)

TSV-format counts matrix, normalised to size factors

normalised_counts.tsv

variance_stabilised_counts (file)

TSV-format counts matrix, normalised to size factors, with variance stabilisation applied

variance_stabilised_counts.tsv

model (file)

TXT-format DESeq2 model

deseq2.model.tsv

versions (file)

File containing software versions

versions.yml