--reference options doesn't override the reference genomes in a CRAM file

[bcantarel]

I was trying to run sniffles in a workflow, where the alignments and variant calls are done on separate VMs.

I get an error that it can't find the genome.fa file (gives the path from the alignment work directory) even though I pass that file as --reference genome.fa.

If I convert the cram file to cram using samtools with the local genome.fa ie
samtools view -@ ${threads} -C -T genome/genome.fa -o test.cram original.cram
samtools index -@ ${threads} test.cram

With the new cram sniffles runs without error.

[fritzsedlazeck]

@hermannromanek is that fixed? maybe we can just close this?