Updating picard to 3.2.0 fails pipeline level tests

[maxulysse]

          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 https://github.com/nf-core/rnaseq/issues/1335#issuecomment-2242357830

[maxulysse]

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

[maxulysse]

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

[lldean18]

Hi, is this issue resolved now? I am getting the same warning message.

[pinin4fjords]

Should have been resolved in https://github.com/nf-core/rnaseq/pull/1335, please reopen if this is present in newer pipeline versions