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Is your feature request related to a problem? Please describe.
See the setup for my bug report "Using option --drmaa_logs crashes snakemake #2819" except the profile config.yaml looks now as follows:
(snakemake-tutorial-v8+) $ snakemake --cores 1 --use-conda --profile drmaa
Using profile drmaa for setting default command line arguments.
Building DAG of jobs...
Your conda installation is not configured to use strict channel priorities. This is however crucial for having robust and correct environments (for details, see https://conda-forge.org/docs/user/tipsandtricks.html). Please consider to configure strict priorities by executing 'conda config --set channel_priority strict'.
Using shell: /usr/bin/bash
Provided remote nodes: 100
Job stats:
job count
--------- -------
map_reads 1
total 1
Select jobs to execute...
InputFunctionException in rule map_reads in file <path to snakemake-tutorial>/snakemake-tutorial-v8+/snakemake-snakemake-tutorial-data-be6ae5a/Snakefile, line 1:
Error:
WorkflowError:
Failed to evaluate resources value ''.
String arguments may need additional quoting. E.g.: --default-resources "tmpdir='/home/user/tmp'" or --set-resources "somerule:someresource='--nice=100'". This also holds for setting resources inside of a profile, where you might have to enclose them in single and double quotes, i.e. someresource: "'--nice=100'".
SyntaxError: invalid syntax (<string>, line 0)
Wildcards:
Traceback:
(rule map_reads, line 1, <path to snakemake-tutorial>/snakemake-tutorial-v8+/snakemake-snakemake-tutorial-data-be6ae5a/Snakefile)
(snakemake-tutorial-v8+) $
Describe the solution you'd like
I would like SnakeMake to accept empty default resources
Describe alternatives you've considered
Provide an option that I would specify directly in "drmaa_option", e.g. -V as an additional_drmaa_options
The text was updated successfully, but these errors were encountered:
sven0schuierer
changed the title
Add possibility to provide empty default resources in a profles (as was possible with SnakeMake 7.x.x)
Add possibility to provide empty default resources in a profile (as was possible with SnakeMake 7.x.x)
Apr 18, 2024
Is your feature request related to a problem? Please describe.
See the setup for my bug report "Using option --drmaa_logs crashes snakemake #2819" except the profile config.yaml looks now as follows:
If I run SnakeMake as in the bug report, I get:
Describe the solution you'd like
I would like SnakeMake to accept empty default resources
Describe alternatives you've considered
Provide an option that I would specify directly in "drmaa_option", e.g. -V as an additional_drmaa_options
The text was updated successfully, but these errors were encountered: