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I have a workflow that runs correctly on my own machine, but fails when being submitted to a cluster. The error seems to be a shell problem on the jobscript written where the environment variables are set:

/nfs/mypath/test/.snakemake/tmp.m80omc9q/snakejob.retrieve_data.3.sh: 
line 3: NEW_ACCESSION='E-CORN-1' ACCESSIONS='E-MTAB-4395,E-MTAB-4342,E-MTAB-4128,E-MTAB-3826,E-MTAB-3173,E-MTAB-964,E-GEOD-62778,E-GEOD-54272' 
COVARIATE_TYPE='characteristic' 
BATCH='study' COVARIATE='organism part' 
CACHE_PATH='/other-path/baseline-merge-cache': No such file or directory

however, because the jobscript gets deleted, I cannot check the shell script to understand the issue. Is there any way of keeping this file after snakemake finishes/fails for inspection?

pablacious
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    I realise that this might be partly a duplicate of https://stackoverflow.com/questions/47645990/how-to-keep-the-snakemake-shell-file-while-running-in-cluster, but no one indicates how to keep the file there. – pablacious May 21 '21 at 14:02

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