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DSL2 Metagenomics - Update the test-datasets and input-files for test profiles #1085

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merszym opened this issue Sep 6, 2024 · 2 comments · May be fixed by #1113
Open

DSL2 Metagenomics - Update the test-datasets and input-files for test profiles #1085

merszym opened this issue Sep 6, 2024 · 2 comments · May be fixed by #1113
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@merszym
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merszym commented Sep 6, 2024

Problem

We currently use the test-profiles for the metagenomics profilers just as a technical test, that the pipeline runs smootly. But the output is always empty, because the current test-input data (mammoth) and test-databases for the metagenomics profiler tools (bacterial) dont match.

Approach

We should either provide a test-file that has some bacterial reads retained after host-removal or update the test-databases to have some "real" tables produced as output after the end of the respective test-runs.

@merszym merszym added bug Something isn't working small_fix labels Sep 6, 2024
@merszym merszym added DSL2 and removed bug Something isn't working labels Sep 6, 2024
@merszym
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merszym commented Jan 24, 2025

Waiting for now to incorporate the tests in the new nf-test framework

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merszym commented Jan 31, 2025

Classifier Input-Fasta Database TODO?
Krakenuniq Mammoth Mammoth DONE
Kraken2 Mammoth contains Mammoth Nothing
Metaphlan Mammoth To check To check
Malt Mammoth contains Mammoth Nothing

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