Description

Runs a differential expression analysis with dream() from variancePartition R package

Input

name:type
description
pattern

meta:map

Groovy Map containing run and contrast information.

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

formula:string

(Mandatory) R formula string used for modeling, e.g. ’~ treatment + (1 | sample_number)’.

meta2:map

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

samplesheet:file

Sample sheet file containing sample metadata.

counts:file

TSV or CSV format expression matrix with genes as rows and samples as columns.

Output

name:type
description
pattern

results

meta:map

groovy array with metadata information for the contrast generated

*.dream.results.tsv:file

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

*.dream.results.tsv

model

meta:map

Metadata map passed through from input.

*.dream.model.txt:file

R model description text file.

*.dream.model.txt

versions

versions.yml:file

File containing software versions

versions.yml