Ungzipped GTF created in PREPARE_GENOME subworkflow not being used

[nschcolnicov]

Description of the bug

I recently came across this error during the execution of this process "NFCORE_RNAVAR:RNAVAR:FASTQ_ALIGN_STAR:STAR_ALIGN":

It seems that the process is complaining about the GTF file not being unzipped, but this is being done in the PREPARE_GENOME subworkflow:

However, this is being overwritten in the main.nf file:

This line should be change to be the same as for the ch_fasta, and ch_star_index, (ch_gtf = PREPARE_GENOME.out.gtf) else the ch_gtf is being populated by the gzipped version of the gtf file, whenever the params.gtf is true.

UPDATE:
When looking into this issue, I also saw that the ch_fast_fai was also creating an issue, because it was now containing an additional meta map https://github.com/nf-core/rnavar/blob/dev/main.nf:

This created issues because the channel also gets added a meta map in some of the modules i.e https://github.com/nf-core/rnavar/blob/dev/subworkflows/local/splitncigar/main.nf:

This caused the channel to become a tuple of two meta maps and 1 fasta_fai index, which caused issues in the pipeline execution

All of these new issues seem to have been introduced in this PR: #140

Command used and terminal output

No response

Relevant files

No response

System information

No response

[nschcolnicov]

PR was merged, closing this issue