No output for bf-fetch seq when given a RefSeq accession

[dagsdags212]

Description

Running the seq subcommand from the bf-fetch module does not generate an output directory when given a RefSeq accession. It runs without issues and produces no error code.

Replicate

Run the following commands:

micromamba activate bf-fetch
bf-fetch seq ACC=GCA_003032905.1 

Expected behavior

Running ls would show a uncompressed directory named GCC_003032905 containing the reference genome

Actual behavior

The named directory is missing.

[dagsdags212]

I found the issue.

Bug Description

When running install.sh, aliases that point to the target directory are created ($HOME/.local/share/bioflow/src/<module>). Upon invoking a bf-fetch command, the scripts execute within the context of the target directory and thus data end of being saved here.

Proposed Solution

• provide an option to specify the path where data will be stored
• by default, data should be stored in your current working directory