Confusing Info Printout about GFF and GTF

[subwaystation]

When I run the pipeline using an iGenomes genome, the pipelines informs me, that GTF is favoured over GFF and that the GFF will be ignored, although I never specified a GFF. Furthermore, iGenomes provides a GTF for EB1 as can be seen in https://github.com/nf-core/rnaseq/blob/master/conf/igenomes.config.
Nextflow start:

nextflow run nf-core/rnaseq -r dev --reads '*.fastq.gz' --genome EB1 -profile cfc --singleEnd

Confusing message:

...
Prefer GTF over GFF, so ignoring provided GFF in favor of GTF
...

I think one should either not print this message or at least I would like to know what is going on :)

[apeltzer]

I think that means to say whatever you provide as GTF is overruling any specified GFF file (as GFF -> GTF conversion loses some info in most cases..).

[apeltzer]

Was adjusted in V1.4 which was just now released 👍

[drpatelh]

This hasnt been updated in the latest release. I agree, it is a bit confusing.

[apeltzer]

The text was, but the message logic not ;-)

[drpatelh]

Ok. This whole block is confusing and will need a proper look. Indenting doesnt help either 😅

rnaseq/main.nf

Lines 259 to 288 in 55eee0c

	if( params.gtf ){
	if ( params.gff ){
	// Prefer gtf over gff
	log.info "nf-core/rnaseq prefers a GTF over GFF, so ignoring a provided GFF in favor of GTF"
	}
	if (hasExtension(params.gtf, 'gz')){
	gtf_gz = Channel
	.fromPath(params.gtf, checkIfExists: true)
	.ifEmpty { exit 1, "GTF annotation file not found: ${params.gtf}" }
	} else {
	Channel
	.fromPath(params.gtf, checkIfExists: true)
	.ifEmpty { exit 1, "GTF annotation file not found: ${params.gtf}" }
	.into { gtf_makeSTARindex; gtf_makeHisatSplicesites; gtf_makeHISATindex; gtf_makeSalmonIndex; gtf_makeBED12;
	gtf_star; gtf_dupradar; gtf_qualimap; gtf_featureCounts; gtf_stringtieFPKM; gtf_salmon; gtf_salmon_merge }
	}
	} else if ( params.gff ){
	if (hasExtension(params.gff, 'gz')){
	gff_gz = Channel.fromPath(params.gff, checkIfExists: true)
	.ifEmpty { exit 1, "GFF annotation file not found: ${params.gff}" }
	} else {
	gffFile = Channel.fromPath(params.gff, checkIfExists: true)
	.ifEmpty { exit 1, "GFF annotation file not found: ${params.gff}" }
	}
	} else {
	exit 1, "No GTF or GFF3 annotation specified!"
	}

Im going to remove this message here because the gff and gtf validation is done earlier anyway:

rnaseq/main.nf

Lines 655 to 657 in 55eee0c

	} else {
	log.info "Prefer GTF over GFF, so ignoring provided GFF in favor of GTF"
	}

[apeltzer]

Yeah, this isn't optimal

[drpatelh]

Fixed in #319