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When the workflow makes use of environment variables (by declaring them in envvars and then using them through os.environ), the workflow execution fails on batch schedulers because the jobscript gets the variable split by the space (it needs quoting).
Look at COVARIATE below
/nfs/my-path/.snakemake/tmp.fjbaxuov/snakejob.retrieve_data.3.sh: line 3: CACHE_PATH=/my-path/cache 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 BATCH=study NEW_ACCESSION=E-CORN-1 COVARIATE=organism part COVARIATE_TYPE=characteristic: No such file or directory
Run any workflow that uses an env variable that has a space in the value in a cluster environment. On a local execution (no cluster), there is no issue.