fix: declare associative arrays in bash scripts #1844
Merged
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description
This PR adds a hotfix for bash scripts. I don't know if this is a Bash version issue or not, but when I tried to run a bash script on v4.4.20 (I tested the implementation of bash scripts with v5.1.16) the named variabes were playing up.
Here is an example to illustrate the problem (I've removed
snakemake_config
for brevity)when this script was executed, it was failing with
/hps/nobackup/iqbal/mbhall/drprg/paper/.snakemake/scripts/tmpbf4avsq5.tbprofiler_predict.sh: line 16: reads: unbound variable
.But when I explicitly declare the snakemake variables as associative arrays (
declare -A
), the script ran fine.I'm not quite sure what the root cause of the problem is, but declaring the snakemake variables fixes the problem so that seems sufficient I guess?
QC
docs/
) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).