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bihealth / seasnap-pipeline

SeA-SnaP: (Se)q (A)nalysis (Sna)kemake (P)ipeline
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--config file_name="..." doesn't work if DE_config.yaml and covariate_file.txt are not present #11

Open january3 opened 2 years ago

january3 commented 2 years ago

Normally, one can change the default yaml file with the sea-snap configuration using the snakemake option --config file_name"..."

This works correctly only if the default files are also present in the current directory. These files are not used, however.

To replicate: move the file DE_config.yaml to DE_config.yaml_foo and run `sea-snap DE l --config file_name="DE_config.yaml_foo" -j1

This will exit with an error.

messersc commented 2 years ago

Would DE_config_foo.yaml work? Maybe the file extension is the problem?