--aligner bwameth samtools sort bam incorrectly named with deduplicated prefix

[tylerstahl]

Description of the bug

When using --aligner bwameth samtools sort will label output bams with prefix "${meta.id}.deduplicated.sorted" and publish in the deduplication folder

related to issue #579

Command used and terminal output

nextflow run nf-core/methylseq -r 4.1.0 -profile test --aligner bwameth --outdir bwa_bug_test

Relevant files

No response

System information

Nextflow 25.10.0
HPC
Slurm 24.05.0
Apptainer 1.4.1
RHEL 9.4
nf-core/methylseq 4.1.0

[sateeshperi]

@tylerstahl I don't get what is the issue you have here. Could you kindly elaborate and why you think its a bug?

[tylerstahl]

Hi @sateeshperi ! Yes, and please correct me, if I am wrong. When using bwameth as the aligner, the bam files never get deduplicated before passing to samtools sort. However, the samtool sort output uses the deduplicated prefix.

This seems to be a issue with samtools sort config, where ext.prefix = params.skip_deduplication ? { "${meta.id}.sorted" } : { "${meta.id}.deduplicated.sorted" } is only enabled when params.skip_deduplication is true.

[sateeshperi]

yes I see now. It works for Bismark workflow as dedup happens there first. going to send in a fix. Thank you!

[tylerstahl]

@sateeshper Similar issue for #579 where params.rrbs should also be included in the conditional logic

[sateeshperi]

Yes has been fixed in current dev. Kindly check and confirm

[sateeshperi]

fixed from v4.2.0