Modularise the code base and add HPC automated checks - Githubissues

georgiesamaha / configBuilder-nf

Nextflow config builder scripts for supported HPC infrastructures.

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Modularise the code base and add HPC automated checks #11

Closed georgiesamaha closed 11 months ago

georgiesamaha commented 11 months ago

Only working on custom (non-nfcore) pipeline pathway. Have not made changes to nf-core pathway.

Modularised code base (as per #10):

Renamed existing module custom_pipeline (previously nxfconfigBuilder)
Split out new modules:create_container, create_resources, hpc_env
TODO: create additional modules for cloud env configuration, local env configuration

Added functionality to hpc env configuration (as per #5 and #6):

Auto check for schedulers: only slurm, pbspro, sge
Auto check for module and if so, check if singularity is available

georgiesamaha commented 11 months ago

@jfy133 should be easier for us to work on this now. Have tried out your automated identification of scheduler, singularity module, works nicely :)