Description

validate consistency of feature and sample annotations with matrices and contrasts

Input

name:type
description
pattern

meta

:map

Groovy Map containing information on experiment, at a minimum an id. e.g. [ id:‘test’ ]

sample

:file

CSV-format sample sheet with sample metadata

assay_files

:file

List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised).

meta2

:map

Groovy Map containing information on features. e.g. [ id:‘test’ ]

feature_meta

:file

TSV-format feature (e.g. gene) metadata

meta3

:map

Groovy Map containing information on contrasts. e.g. [ id:‘test’ ]

contrasts

:file

CSV-format file with four columns identifying the sample sheet variable, reference level, treatment level, and optionally a comma-separated list of covariates used as blocking factors.

Output

name:type
description
pattern

sample_meta

meta

:map

Groovy Map containing information on experiment. e.g. [ id:‘test’ ]

*/*.sample_metadata.tsv

:file

File containing validated sample metadata

/*.sample_metadata.tsv

feature_meta

meta

:map

Groovy Map containing information on experiment. e.g. [ id:‘test’ ]

*/*.feature_metadata.tsv

:file

File containing validated feature metadata

/*.feature_metadata.tsv

assays

meta

:map

Groovy Map containing information on experiment. e.g. [ id:‘test’ ]

*/*.assay.tsv

:file

Files containing validated matrices

/*.assay.tsv

contrasts

meta

:map

Groovy Map containing information on experiment. e.g. [ id:‘test’ ]

*/*.contrasts_file.tsv

:file

Files containing validated matrices

/*.contrasts_file.tsv

versions_shinyngs

${task.process}

:string

The name of the process

shinyngs

:string

The name of the tool

Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))"

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

shinyngs

:string

The name of the tool

Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))"

:eval

The expression to obtain the version of the tool

Tools

shinyngs
AGPL v3

Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion.

github.com/pinin4fjords/shinyngs rawgit.com/pinin4fjords/shinyngs/master/vignettes/shinyngs https://github.com/pinin4fjords/shinyngs
included in
differentialabundance
maintainer
Github user pinin4fjords
get in touch
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