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
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
Output
name:type
description
pattern
results_genewise{:bash}
meta{:bash}
:file
TSV-format table of genes associated with differential expression
information as compiled from the propd results
*.propd.genewise.tsv
*.propd.genewise.tsv{:bash}
:file
TSV-format table of genes associated with differential expression
information as compiled from the propd results
*.propd.genewise.tsv
genewise_plot{:bash}
meta{:bash}
:file
TSV-format table of genes associated with differential expression
information as compiled from the propd results
*.propd.genewise.tsv
*.propd.genewise.png{:bash}
:file
PNG-format plot of accumulated between group variance vs median log
fold change. Genes with high between group variance and high log fold
change are likely to be differentially expressed.
*.propd.genewise.png
rdata{:bash}
meta{:bash}
:file
TSV-format table of genes associated with differential expression
information as compiled from the propd results
*.propd.genewise.tsv
*.propd.rds{:bash}
:file
(Optional) R data containing propd object
*.propd.rds
results_pairwise{:bash}
meta{:bash}
:file
TSV-format table of genes associated with differential expression
information as compiled from the propd results
*.propd.genewise.tsv
*.propd.pairwise.tsv{:bash}
:file
(Optional) TSV-format table of the native propd pairwise results. This
table contains the differential proportionality values associated to
each pair of genes.
*.propd.pairwise.tsv
results_pairwise_filtered{:bash}
meta{:bash}
:file
TSV-format table of genes associated with differential expression
information as compiled from the propd results
*.propd.genewise.tsv
*.propd.pairwise_filtered.tsv{:bash}
:file
(Optional) TSV-format table of the filtered propd pairwise results. This
table contains the pairs of genes with significant differential
proportionality values.
*.propd.pairwise_filtered.tsv
adjacency{:bash}
meta{:bash}
:file
TSV-format table of genes associated with differential expression
information as compiled from the propd results
*.propd.genewise.tsv
*.propd.adjacency.csv{:bash}
:file
(Optional) CSV-format table of the adjacency matrix defining a graph, with
edges (1) associated to pairs of genes that are significantly differentially
proportional.
*.propd.adjacency.csv
fdr{:bash}
meta{:bash}
:file
TSV-format table of genes associated with differential expression
information as compiled from the propd results
*.propd.genewise.tsv
*.propd.fdr.tsv{:bash}
:file
(Optional) TSV-format table of FDR values. When permutation tests is performed,
this table is generated with the FDR values calculated by the permutation tests.
This is a more conservative test than the default BH method, but more
computationally expensive.
