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nf-core / rnavar

gatk4 RNA variant calling pipeline
https://nf-co.re/rnavar
MIT License
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Ungzipped GTF created in PREPARE_GENOME subworkflow not being used #148

Closed nschcolnicov closed 4 months ago

nschcolnicov commented 4 months ago

Description of the bug

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

It seems that the process is complaining about the GTF file not being unzipped, but this is being done in the PREPARE_GENOME subworkflow: image However, this is being overwritten in the main.nf file: image

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: image 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: image 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: https://github.com/nf-core/rnavar/pull/140

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nschcolnicov commented 4 months ago

PR was merged, closing this issue