Using gff annotation file input instead of gtf input leads to error "No such variable: gtfFile"

[orangebromeliad]

Hi Team,

I recently ran the pipeline using a gff file for genome annotation and encountered the following error:

No such variable: gtfFile
 -- Check script '/camp/home/littlet/.nextflow/assets/nf-core/rnaseq/main.nf' at line: 774 or see '.nextflow.log' file for more details

After asking on the Slack, Harshil Patel pointed out that this may be due to a bug around line 774 which doesn't check whether a gtf file is provided or not, and thus the program fails when a gtf file cannot be found.

rnaseq/main.nf

Line 774 in 4a0eeb4

gtfFile.into{ gtf_makeSTARindex; gtf_makeHisatSplicesites; gtf_makeHISATindex;

Here is my command by the way:

nextflow run nf-core/rnaseq -profile crick\
	--reads '/camp/lab/langhornej/working/HPC/littlet/audrey24h-reads-symlink/*{1,2}.fastq.gz' \
	--fasta '/camp/lab/langhornej/working/HPC/littlet/tlittle-PUF-symlink/genomes/PlasmoDB-45_Pchabaudichabaudi_Genome.fasta' \
	--gff '/camp/lab/langhornej/working/HPC/littlet/tlittle-PUF-symlink/genomes/PlasmoDB-45_Pchabaudichabaudi.gff' \
	--aligner 'hisat2' \
	--hisat2_index '/camp/lab/langhornej/working/HPC/littlet/tlittle-PUF-symlink/genomes/chabaudi_45_genome.' \
	--fc_extra_attributes false --fc_group_features 'gene_id' --fc_count_type 'exon' --skipBiotypeQC \
	-r dev

Thanks in advance! For now I'm going to follow advice and convert to a gtf file.

Tim

[drpatelh]

Should be fixed when 85afde7 is merged into dev @orangebromeliad