fix probe-set inclusion assertion - #12601
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mahesh-panchal
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mahesh-panchal
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Can you add nf-tests for this change please?
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Hi @mahesh-panchal ; But also, added a new test for mimicking the pipeline scenario where we might have multiple references loaded for samples with different library types, and thus, avoid loading the reference for the mutually exclusive types. Example added is CMO with probeset frna present ... but then, module should not load it in the execution. |
| process.out.outs[0][1].findAll { file(it).name == 'cells_per_tag.json' }, | ||
| process.out.outs[0][1].findAll { file(it).name.contains('metrics_summary.csv') }, | ||
| process.out.outs[0][1].findAll { file(it).name.contains('sample_filtered_feature_bc_matrix.h5') } | ||
| ).match() |
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Can you add asserts on the config please to ensure they contain certain key words?
{ assert !path(process.out.config[0][1]).text.contains('probe-set,') }
This would also help the other tests too.
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Hi @mahesh-panchal ,
Sure, I can do that.
Sorry for the late reply, I was on holidays.
Will start it tomorrow.
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Resolves #12600
Updating the
frnaprobes-set reference assertion.It was seen when running the
nf-core/scrnaseqpipeline test dataset, that the probe-set was still being included even though data wascmo.