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update module: PERBASE #9795

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@camlloyd camlloyd commented Jan 28, 2026

PR checklist

Closes #9794 by bumping perbase version and using topic channels

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Broadcast software version numbers to topic: versions - See version_topics
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  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
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      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
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@camlloyd camlloyd changed the title Perbase update module: PERBASE Jan 28, 2026
mashehu
mashehu approved these changes Jan 28, 2026
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modules/nf-core/perbase/tests/main.nf.test.snap
"id": "test",
"single_end": false
},
"test.tsv.gz:md5,a18ee6e481ab7cbad3c3a9f71465b904"
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@mashehu mashehu Jan 28, 2026

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Any idea why the results changed in the new version?

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@camlloyd camlloyd Jan 28, 2026

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One explanation is the COUNT_OF_MATE_RESOLUTIONS column that was introduced in version 1.1.0.

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@camlloyd camlloyd Jan 28, 2026

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Let's investigate how the output looks.

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@camlloyd camlloyd Jan 29, 2026 •
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Before:

REF POS REF_BASE DEPTH A C G T N R Y S W K M INS DEL REF_SKIP FAIL NEAR_MAX_DEPTH
chr21 5011214 T 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 False
chr21 5011215 C 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 False
chr21 5011216 A 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False
chr21 5011217 A 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False
chr21 5011218 T 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 False
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
chr21 46664973 T 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 False
chr21 46664974 A 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False
chr21 46664975 T 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 False
chr21 46664976 A 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False
chr21 46664977 T 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 False

1558238 rows × 20 columns

After:

REF POS REF_BASE DEPTH A C G T N R ... S W K M INS DEL REF_SKIP FAIL COUNT_OF_MATE_RESOUTIONS NEAR_MAX_DEPTH
chr21 5011214 T 1 0 0 0 1 0 0 ... 0 0 0 0 0 0 0 0 0 False
chr21 5011215 C 1 0 1 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 False
chr21 5011216 A 1 1 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 False
chr21 5011217 A 1 1 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 False
chr21 5011218 T 1 0 0 0 1 0 0 ... 0 0 0 0 0 0 0 0 0 False
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
chr21 46664973 T 2 0 0 0 2 0 0 ... 0 0 0 0 0 0 0 0 0 False
chr21 46664974 A 2 2 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 False
chr21 46664975 T 2 0 0 0 2 0 0 ... 0 0 0 0 0 0 0 0 0 False
chr21 46664976 A 2 2 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 False
chr21 46664977 T 1 0 0 0 1 0 0 ... 0 0 0 0 0 0 0 0 0 False

1558238 rows × 21 columns

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@camlloyd camlloyd Feb 5, 2026 •
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In fact, there is a typo in the output column COUNT_OF_MATE_RESOUTIONS. This should be fixed in version 1.3.0, but it isn't available on bioconda yet.

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update module: PERBASE

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