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jts / ncov-tools

Small collection of tools for performing quality control on coronavirus sequencing data and genomes
MIT License
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Add configurable optional output directory #80

Closed fmaguire closed 3 years ago

fmaguire commented 3 years ago

Add an optional output_dir value that specifies a directory to output results into.

To ensure that relative paths to input files/resources in config.yaml are still valid when output_dir is specified, the relevant values are resolved to absolute paths if present in the config.yaml.

If output_dir isn't specified then the output_dir/workdir is just the directory that snakemake is executed from i.e., the current working directory will be used (as is the current behaviour) and no other changes are made.

Changes have been tested for conda env install.

jts commented 3 years ago

@rdeborja could you test this locally?