georgiesamaha / configBuilder-nf

Nextflow config builder scripts for supported HPC infrastructures.
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Fix broken autodetection of PBSpro schedulder #45

Closed georgiesamaha closed 8 months ago

georgiesamaha commented 8 months ago

Unable to test this on other systems at this stage. When trying to autodetect PBSpro as scheduler, returns 'none', despite qstat --version running fine in the shell. Thought the inconsistency may have something to do with how command output is handled in the shell vs with subprocess.run. Have updated create_hpc_env.py to fix this.

Could you please test and let me know if it breaks anything for you?