No results are copied to any output directory

[szilvajuhos]

After a successful run they are staying in the work/... directory. When using /scratch it means we are loosing the results altogether. Command line was:
nextflow run /home/szilva/sarek/default/somaticVC.nf -profile singularityPath --tools strelka --genome GRCh38 --genome_base /sw/data/uppnex/ToolBox/hg38bundle --sample Preprocessing/Recalibrated/recalibrated.tsv --containerPath /home/szilva/sarek/containers/ --noReports --verbose

[szilvajuhos]

Looks it ts true for other tools as well.

[maxulysse]

OK,
I'll look into it ASAP.
Thanks for noticing that...

[maxulysse]

Results from germlineVC.nf are copied to the VariantCalling directory.
So the problem should be easy to find and to fix.

[maxulysse]

Working well on my case.
Can't seem to reproduce your problem @szilvajuhos

[szilvajuhos]

Made a test set from the DREAM challenge using only chr22 that can be found on irma at /lupus/proj/ngi2016004/private/szilva/sarek_test . There is a runTool.sh script to launch Sarek, and it was like
/lupus/proj/ngi2016004/private/szilva/sarek_test $ ./runTool.sh freebayes 2>&1 | tee fb.log
The interval file is changed so it is going through only a 1M bps part .
Looks everythong is OK, even the ConcatVCF part is ready, but the results are not copied to the final destination.

[maxulysse]

OK, so definitively this problem seems to be specific at Irma and Bianca.
I'll go CSI mode and investigate it out 🔍.