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Updating picard to 3.2.0 fails pipeline level tests #1346

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maxulysse opened this issue Jul 22, 2024 · 2 comments · Fixed by #1335
Open

Updating picard to 3.2.0 fails pipeline level tests #1346

maxulysse opened this issue Jul 22, 2024 · 2 comments · Fixed by #1335

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@maxulysse
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          New error coming out of Picard:

A field field parsed out of a read name was expected to contain an integer and did not. Read name: SRR6357072.6014972. Cause: String 'SRR6357072.6014972' did not start with a parsable number.

Originally posted by @maxulysse in #1335 (comment)

@maxulysse
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Issue is most likely due to read group names coming from the test data, could be probably be solved with some smart args

cf https://gatk.broadinstitute.org/hc/en-us/community/posts/360074797471-Read-Names-of-Public-Fastq-Files-incompatible-with-Picard-s-MarkDuplicates

@pinin4fjords pinin4fjords linked a pull request Aug 20, 2024 that will close this issue
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@maxulysse
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This is currently fixed by a patch that keep the same version of picard, but issue is most likely still there and will need fixing in future update, so let's keep this issue open for now

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