--rrbs samtools sort bam incorrectly named with deduplicated prefix

[tylerstahl]

Description of the bug

I noticed when using the --rrbs parameter bismark deduplication gets skipped but samtools sort uses the prefix "${meta.id}.deduplicated.sorted" and published in the deduplication folder

Command used and terminal output

nextflow run nf-core/methylseq -r 4.1.0 -profile test --rrbs --outdir rrbs_bug_test

Relevant files

samtools sort command
command.sh

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]

fixed in v4.2.0