so RX tags are copied for UMIs

[lnblum]

relies on this change to bwameth, so will need to wait for bioconda release or use another installation.
brentp/bwa-meth@2bf5ae3

[Copilot]

Pull request overview

Updates the trimming step so that UMI information stored in the BAM RX tag can be carried through BAM→FASTQ conversion (and then through fastp) by explicitly copying RX into FASTQ output.

Changes:

• Bump fastp conda dependency from 1.0.1 to 1.1.0.
• Remove the fastp_path override and invoke fastp directly from the environment.
• Update samtools fastq invocation to attempt to copy RX tags into FASTQ (-T RX).

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

File	Description
modules/fastp.nf	Update fastp/samtools invocation to preserve RX tag during BAM→FASTQ→fastp trimming.
conf/test.config	Remove unused fastp_path param from the test profile.

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[bwlang]

@lnblum this seems like a good thing to fix...

[lnblum]

Probably the test is failing because the snapshot needs to be updated for the fastp version change (which gets us back to the bioconda fastp rather than our local install since the adapter dimer fix was merged). But I'm waiting on the bwameth change -- until then this UMI fix won't work and it breaks.

[bwlang]

i re-ran the tests... i think they are failing due to the fastp version difference:

"\t\t"fastp_version": "1.0.1",", | "\t\t"fastp_version": "1.1.0",",

[lnblum]

i re-ran the tests... i think they are failing due to the fastp version difference:

"\t\t"fastp_version": "1.0.1",", | "\t\t"fastp_version": "1.1.0",",

@bwlang Yes, I agree, thanks! UMI fix won't work without the bwameth change. I'm still hoping that goes into conda soon, but if we need it before then a local version of bwameth could be used.