Merged Replicates-Feature counts does not use the merged bams

[SuhasSrinivasan]

Description of the bug

Dear Authors,

Thank you for developing and maintaining this pipeline.

There is a potential issue with the merged replicates, as it is not clear why Task 6.7 is defined as Count reads in consensus peaks relative to merged library-level alignments.

Below is the executed task

Program:featureCounts v2.0.1; Command:"featureCounts" "-F" "SAF" "-O" "--fracOverlap" "0.2" "-p" "-T" "6" "-a" "consensus_peaks.mRp.clN.saf" "-s" "0" "-o" "consensus_peaks.mRp.clN.featureCounts.txt" "D6_T_REP2.mLb.clN.sorted.bam" "D6_T_REP1.mLb.clN.sorted.bam" "D6_D_REP2.mLb.clN.sorted.bam" "D6_D_REP1.mLb.clN.sorted.bam" "D6_M_REP2.mLb.clN.sorted.bam" "D6_M_REP1.mLb.clN.sorted.bam"

Should this not be using the merged replicate BAMs?

Program:featureCounts v2.0.1; Command:"featureCounts" "-F" "SAF" "-O" "--fracOverlap" "0.2" "-p" "-T" "6" "-a" "consensus_peaks.mRp.clN.saf" "-s" "0" "-o" "consensus_peaks.mRp.clN.featureCounts.txt" "D6_T.mRp.clN.sorted.bam" "D6_D.mRp.clN.sorted.bam" "D6_M.mRp.clN.sorted.bam"

Command used and terminal output

Relevant files

No response

System information

Version of nf-core/atacseq: 2.1.2
Nextflow version: v24.10.3
Container engine: Docker 27.4.1
OS: Ubuntu 22.04.5 LTS x86_64
Executor: Local
Hardware: Desktop