nf-core
Bowtie2 + Samtools pipeline in nf-core module may use double the intended threads
Have you checked the docs?
Description of the bug
In the nf-core Bowtie2 alignment module, the pipeline runs something like:
bowtie2 ... --threads $task.cpus ... | samtools ... --threads $task.cpus ...
Because Bowtie2 and Samtools are piped, both programs seem to independently use $task.cpus threads.
I observed this when I was running nf-core/atacseq, and the bowtie_align step was using more cores than it is supposed to use. When inspecting processes with htop, I saw a bowtie2 process and a samtools process, both using 12 threads, and I had only given 12 threads to this process. I scheduled the process with slurm on our cluster.
Should this be solved by making sure that bowtie2 and samtools both ask for less threads than $task.cpus?
Command used and terminal output
Relevant files
No response
System information
nextflow 25.10.0 run on our HPC with slurm executor container engine: singularity CentOS Linux release 7.4 running the dev branch of nf-core/atacseq, which uses the bowtie2_align module
