pVACbind_class_I subjobs successfully run after re-setting tmp folder

[mingwhy]

Hi ausserh,

I read in the readme file that

The modules pVACbind_class_I and pVACbind_class_II may occasionally fail for one subjob while the others work fine. If this occurs, try resuming the run; the failed subjob should complete on the next attempt.

It indeed happend when I was using this pipeline.
I checked the .command.log file in detail using working folder path from .nextflow.log and found the error message to be: No space left on device: '/tmp/tmprq6ohhdc'.

Given this case, I reset tmp folder to a local, mucher bigger path, then all pVACbind_class_I subjobs ran successfully.

export TMPDIR=/mnt/lab/usera_name/tmp
nohup nextflow -bg run ../../NovumRNA/novumRNA.nf -profile my_profile,singularity --outdir ./ --input_fastq samplesheet.csv -w ./tmp/ -c ../../NovumRNA/novumRNA.config -entry analysis -resume &

Bests!
Ming

[ausserh]

Hi Ming,

thank you for checking this and the provided solution, I will update the README to suggest this.

Best,
Markus