Variant calling step failing when using process scratch

[pditommaso]

When using local scratch folder, the step 5_rnaseq_call_variants returns an error.

This happens because the genome.dict input file contains a reference to a file created in temporary folder not accessible to the task, for example:

# cat genome.dict 
@HD	VN:1.5
@SQ	SN:chr22	LN:51304566	M5:a718acaa6135fdca8357d5bfe94211dd	UR:file:/tmp/nxf.Mzz6eisI1J/genome.fa

[pditommaso]

Tried both:

sed -i 's@UR:file:.*genome.fa@UR:file:genome.fa@g' genome.dict

and

sed -i 's@UR:file:.*genome.fa@UR:file:'"$PWD"'/genome.fa@g' genome.dict

But still reporting:

##### ERROR
##### ERROR MESSAGE: Invalid command line: Cannot process the provided BAM/CRAM file(s) because they were not indexed.  The GATK does offer limited processing of unindexed BAM/CRAMs in --unsafe mode, but this feature is unsupported -- use it at your own risk!