Description

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

Input

Name (Type)
Description
Pattern

meta (map)

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

gtf (file)

An annotation file of the reference genome in GTF format

*.gtf

meta2 (map)

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

quants (directory)

Paths to subdirectories corresponding to sample-wise runs of Salmon or Kallisto

quant_type (string)

Quantification type, ‘kallisto’ or ‘salmon’

id (string)

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

extra (string)

Extra gene attribute in the GTF file (default= gene_name)

Output

Name (Type)
Description
Pattern

meta (map)

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

tx2gene (file)

A transcript/ gene mapping table in TSV format

*.tx2gene.tsv

versions (file)

File containing software versions

versions.yml
included in
circrna riboseq
maintainer
Github user pinin4fjords
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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