fix: declare associative arrays in bash scripts #1844
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johanneskoester
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🤖 I have created a release *beep* *boop* --- ## [7.14.1](v7.14.0...v7.14.1) (2022-09-23) ### Bug Fixes * allocation of local ssds in k8s tests ([#1870](#1870)) ([d0de4dc](d0de4dc)) * allow script directive to take pathlib Path ([#1869](#1869)) ([12cdc96](12cdc96)) * catch errors in remote.AUTO provider list ([#1834](#1834)) ([c613ed2](c613ed2)) * consistently use text output in conda shell commands and various little fixes for failing test cases due to conda package changes ([#1864](#1864)) ([4234fe7](4234fe7)) * declare associative arrays ([#1844](#1844)) ([90ae449](90ae449)) * fix falsely triggered reruns if input files are obtained via workflow.source_path() ([#1862](#1862)) ([2dc2e6a](2dc2e6a)) * fixed typos ([#1847](#1847)) ([a1e49b6](a1e49b6)) * k8s container volume mounts as list ([#1868](#1868)) ([5c54df3](5c54df3)) * None type error when invoking Workflow object manually ([#1731](#1731)) ([dc45ccb](dc45ccb)) * request disk_mb resource from k8s ([#1858](#1858)) ([f68f166](f68f166)) * respect shebang lines in post-deploy scripts (see deployment docs) ([#1841](#1841)) ([c26c4b6](c26c4b6)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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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_configfor 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).