Description

Filters a differential expression table based on logFC and adjusted p-value thresholds

Input

name:type
description
pattern

meta

:map

Groovy Map containing sample information e.g. [ id:β€˜test’, single_end:false ]

input_file

:file

Input differential expression table (CSV, TSV, or TXT format)

*.{csv,tsv,txt}

logfc_column

:string

Name of the column containing log fold change values

fc_threshold

:float

Fold change threshold for filtering

fc_cardinality

:string

Operator to compare the fold change values with the threshold. Valid values are: ”>=”, ”<=”, ”>”, ”<”.

stat_column

:string

Name of the column containing the significance statistic values (eg. adjusted p-values).

stat_threshold

:float

Statistic threshold for filtering

stat_cardinality

:string

Operator to compare the column values with the threshold. Valid values are: ”>=”, ”<=”, ”>”, ”<”.

Output

name:type
description
pattern

filtered

meta

:map

Groovy Map containing sample information e.g. [ id:β€˜test’, single_end:false ]

*_filtered.tsv

:file

Filtered differential expression table

*_filtered.tsv

filtered_up

meta

:map

Groovy Map containing sample information e.g. [ id:β€˜test’, single_end:false ]

*_filtered_up.tsv

:file

Filtered differential expression table for overexpressed genes

*_filtered_up.tsv

filtered_down

meta

:map

Groovy Map containing sample information e.g. [ id:β€˜test’, single_end:false ]

*_filtered_down.tsv

:file

Filtered differential expression table for underexpressed genes

*_filtered_down.tsv

versions

versions.yml

:file

File containing software versions

versions.yml

Tools

maintainers
Github user pinin4fjords
Github user WackerO
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