bio-miga/miga

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Can't follow non-constant source. Use a directive to specify location.
Open

[[ -s "$MIGA_MOD" ]] && . "$MIGA_MOD"
Severity: Minor
Found in bin/miga-env by shellcheck

Can't follow non-constant source. Use a directive to specify location.

Problematic code:

. "$(find_install_dir)/lib.sh"

Correct code:

# shellcheck source=src/lib.sh
. "$(find_install_dir)/lib.sh"

Rationale:

ShellCheck is not able to include sourced files from paths that are determined at runtime. The file will not be read, potentially resulting in warnings about unassigned variables and similar.

Use a [[Directive]] to point shellcheck to a fixed location it can read instead.

Exceptions:

If you don't care that ShellCheck is unable to account for the file, specify # shellcheck source=/dev/null.

Notice

Original content from the ShellCheck https://github.com/koalaman/shellcheck/wiki.

TODO found
Open

    # TODO Implement this check:
Severity: Minor
Found in lib/miga/cli/action/doctor.rb by fixme

TODO found
Open

    # TODO: Find 95%ANI clusters with entries from different species

TODO found
Open

    # TODO: Find AAI values too high or too low for each LCA rank

FIXME found
Open

    # FIXME: Part of the +map_to+ support:
Severity: Minor
Found in lib/miga/remote_dataset.rb by fixme

TODO found
Open

    # TODO: Find different 95%ANI clusters with genomes from the same species
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