Bowtie2 + Samtools pipeline in nf-core module may use double the intended threads

[fbnrst]

Have you checked the docs?

• nf-core website: troubleshooting
• nf-core modules documentation

Description of the bug

In the nf-core Bowtie2 alignment module, the pipeline runs something like:

bowtie2 ... --threads $task.cpus ... | samtools ... --threads $task.cpus ...

see

modules/modules/nf-core/bowtie2/align/main.nf

Lines 57 to 64 in fa14771

	bowtie2 \\
	-x \$INDEX \\
	$reads_args \\
	--threads $task.cpus \\
	$unaligned \\
	$args \\
	2>| >(tee ${prefix}.bowtie2.log >&2) \\
	| samtools $samtools_command $args2 --threads $task.cpus ${reference} -o ${prefix}.${extension} -

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