EF genome broken for hisat2?

[s-andrews]

I tried to run the nf_rnaseq pipeline on the EF4 genome and it died.

nf_rnaseq --genome EF4 SRR453566_yeast_rnaseq.fq.gz

It was the hisat2 which failed and the command nf put together was:

#!/bin/bash -ue
module load hisat2
module load samtools
hisat2 -p 8  --no-unal --no-softclip --new-summary -x null  --known-splicesite-infile /bi/scratch/Genomes/Yeast/Saccharomyces_cerevisiae/EF4/Saccharomyces_cerevisiae.EF4.73.hisat2_splices.txt -U SRR453566_yeast_rnaseq_trimmed.fq.gz  2>SRR453566_yeast_rnaseq_EF4_hisat2_stats.txt | samtools view -bS -F 4 -F 8 -F 256 -> SRR453566_yeast_rnaseq_EF4_hisat2.bam

So the genome index was null, which is bad. Probably a trivial fix though.

[FelixKrueger]

Should work now.