singularity bind paths had an extra trailing quote due to the get_singularity_binds() function, which caused rules to fail while loading the singularity container.
additionally, including the full /lscratch/$SLURM_JOB_ID caused jobs to fail because $SLURM_JOB_ID resolved to the main job's ID, rather than the individual job ID.
this adapts code from RENEE for resolving the bind paths for singularity.
Issues
also resolves #120
PR Checklist
(~Strikethrough~ any points that are not applicable.)
[x] This comment contains a description of changes with justifications, with any relevant issues linked.
~[ ] Update docs if there are any API changes.~
[x] Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/
Changes
singularity bind paths had an extra trailing quote due to the get_singularity_binds() function, which caused rules to fail while loading the singularity container.
additionally, including the full
/lscratch/$SLURM_JOB_IDcaused jobs to fail because$SLURM_JOB_IDresolved to the main job's ID, rather than the individual job ID.this adapts code from RENEE for resolving the bind paths for singularity.
Issues
also resolves #120
PR Checklist
(~Strikethrough~ any points that are not applicable.)
CHANGELOG.mdwith a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/