Closed svarona closed 2 months ago
We are working on a custom gtf file with multiple overlapping features for SARS-CoV-2, but viralrecon won't let you use a gtf file as annotation file.
Depending if the input annotation file is a gff or a gtf, SNPEFF_BUILD process should be changed, because now it only works for gff files: https://github.com/nf-core/viralrecon/blob/23e3441ec70077e5af4717c2ee7d7d0d51f1e77a/modules/local/snpeff_build.nf#L49
Also, some additional changes are needed in the make_variants_long_table.py to allow overlapping features to appear in the results table.
An example of the original variants_long_table output:
An example of the table we want to obtain:
Description of feature
We are working on a custom gtf file with multiple overlapping features for SARS-CoV-2, but viralrecon won't let you use a gtf file as annotation file.
Depending if the input annotation file is a gff or a gtf, SNPEFF_BUILD process should be changed, because now it only works for gff files: https://github.com/nf-core/viralrecon/blob/23e3441ec70077e5af4717c2ee7d7d0d51f1e77a/modules/local/snpeff_build.nf#L49
Also, some additional changes are needed in the make_variants_long_table.py to allow overlapping features to appear in the results table.
An example of the original variants_long_table output:
An example of the table we want to obtain: