Description

Make a transcript/gene mapping from a GTF and cross-reference with transcript quantifications.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing reference information related to the GTF file e.g. [ id:'yeast' ]

gtf{:bash}

:file

An annotation file of the reference genome in GTF format

*.gtf

meta2{:bash}

:map

Groovy Map containing information related to the experiment as a whole e.g. [ id:'SRP123456' ]

quants/*{:bash}

:file

quants file

quant_type{:bash}

:string

Quantification type, ‘kallisto’ or ‘salmon’

id{:bash}

:string

Gene ID attribute in the GTF file (default= gene_id)

extra{:bash}

:string

Extra gene attribute(s) in the GTF file, comma-separated for multiple (default= gene_name)

Output

name:type
description
pattern

tx2gene{:bash}

meta{:bash}

:map

Groovy Map containing reference information related to the GTF file e.g. [ id:'yeast' ]

*tx2gene.tsv{:bash}

:file

A transcript/ gene mapping table in TSV format

*.tx2gene.tsv

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

custom
MIT

"Custom module to create a transcript to gene mapping from a GTF and check it against transcript quantifications"

https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tx2gene/main.nf
included in
circrnariboseqrnaseq
maintainer
Github user pinin4fjords
get in touch
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