nf-core wrapper module for harmonise_xenium.py (nf_xenium_feature_extraction) #3
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| queue = 'normal' | ||
| group = 'cellgeni' | ||
| cpus = 1 | ||
| clusterOptions = '-M 8G -R "select[mem>8G] rusage[mem=8G]"' |
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You can just use the "memory". e.g. "memory = 8.GB"
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I hardcoded this because when using the 'memory', the nf-test.config and tests/nextflow.config files were possibly overriding the configuration from modules.config, which was causing the test to exit with a memory error.
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hmm... but you don't have to use clusteroptions flag, right?
I meant it can be just memory = 8.Gb
| group = 'cellgeni' | ||
| cpus = 1 | ||
| clusterOptions = '-M 8G -R "select[mem>8G] rusage[mem=8G]"' | ||
| container = '/nfs/cellgeni/singularity/images/palom_tiledb.sif' |
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not really required to explicitely declare here I'd say
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This has been removed & pushed now.
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| input[0] = [ | ||
| 'xeniumharmonise_test', // meta map | ||
| '/lustre/scratch127/cellgen/cellgeni/dn10/BK30-SKI-27-FO-3-S3/0043607 - BK30-SKI-27-FO-3-s3 - 2024-10-23 11.28.38.ndpi', |
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how large are these images? Is it possible to upload to s3?
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The image is just being used as a sample for testing the module, and the size is around 36M. Since it's only a sample image, I believe it would be possible to use any other image which we can either upload to S3 or use the one already uploaded.
This PR includes a new nf-core module for
nf_xenium_feature_extractionpipeline wrapping theharmonise_xenium.pyscript as a Nextflow process.Summary:
harmonise_xenium.pyscript within a reproducible Nextflow module.main.nfandmain.nf.testto support the new wrapper module.nf-test.config,modules.config, andnextflow.config.