Description

Generate tables of feature metadata from GTF files

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing information on input GTF file e.g. [ id:‘test’ ]

gtf{:bash}

:file

gtf annotation file

*.{gtf}

meta2{:bash}

:map

Groovy Map containing information in input FASTA file e.g. [ id:‘test’ ]

fasta{:bash}

:file

An optional cDNA file for extracting meta info and/or filtering.

*.{gtf}

Output

name:type
description
pattern

feature_annotation{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.anno.tsv{:bash}

:file

TSV file with feature annotation

*.{tsv}

filtered_cdna{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.fa.gz{:bash}

:file

Where —parse-cdnas is specified in ext.args and an input fasta file is provided, filtered sequences are output to the specified file. No file will be output if this is not specified (for example for use of —dummy-from-cdnas only). See documentation at https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation.

*.{tsv}

versions_atlasgeneannotationmanipulation{:bash}

${task.process}{:bash}

:string

The name of the process

atlas-gene-annotation-manipulation{:bash}

:string

The name of the tool

1.1.1{:bash}

:string

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

atlas-gene-annotation-manipulation{:bash}

:string

The name of the tool

1.1.1{:bash}

:string

The expression to obtain the version of the tool

Tools

atlasgeneannotationmanipulation
Apache-2.0

Scripts for manipulating gene annotation

github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation
included in
differentialabundance
maintainer
Github user pinin4fjords
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