SNIFFLES_SORT_VCF return an error due to mkdtemp

[samuelecancellieri]

Description of the bug

the pipeline runs smoothly until the sniffles sort step.
here bcftools tries to sort the vcf file and this error is returned
mkdtemp(/storage/sahuarea/samuele_cancellieri/general_tmp/8BBQ7N) failed: No such file or directory

i tried to modify the bcftools sort call but the error is not directly related to the sort.
my tmp dir is set by .bashrc on login, so it's not a problem with that also.

thanks a lot for the help.

Command used and terminal output

nextflow run nf-core/nanoseq -r 3.1.0 -profile apptainer -w fei_second_run --max_time 48h --max_cpus 1 --max_memory 512GB --outdir fei_second_run --multiqc_title fei_nanopore_data_merged --input metadata/samplesheet_old.csv --skip_demultiplexing --skip_quantification --protocol DNA --call_variants -resume

the output is ok until the sniffle sort step when this error is returned
mkdtemp(/storage/sahuarea/samuele_cancellieri/general_tmp/8BBQ7N) failed: No such file or directory

Relevant files

nextflow.log.txt
here the log file with the call.
I've tried to modify the bcftools sort call to add the tempdir that i want to be used as tmpdir.

System information

nextflow 24.04.1 build 5913
headless server
executed locally with apptainer
nanoseq -r 3.1.0
OS "Red Hat Enterprise Linux" VERSION="9.4 (Plow)"