Hello! I have just started trying to run the ATAC-seq pipeline locally on my computer and found that trimming was taking a rather long time. In particular, it seemed like the FastQC part of TrimGalore was only running on a single core. In

atacseq/modules/nf-core/trimgalore/main.nf

, the paired-end command for

trim_galore

is:

trim_galore \\
            $args \\
            --cores $cores \\
            --paired \\
            --gzip \\
            ${prefix}_1.fastq.gz \\
            ${prefix}_2.fastq.gz

Checking the TrimGalore manual, it implies that the

--cores

argument is the number of cores used for trimming. There is also a

--fastqc_args "<ARGS>"

option for passing additional arguments to FastQC. As such, maybe this could be incorporated, so as to pass

$cores

(or maybe

$task.cpus

) to the

--threads

argument of FastQC?

Hi! This is how the nf-core module is implemented and I guess it is because, according to trimgalore docs, if

--fastqc_args

is provided then FastQC is always run. If you want to provide this argument you could create and ad-hoc config file that overwrites trimgalore config here and add to your nextflow command

-c custom.config

, something such as:

process {
        withName: 'TRIMGALORE' {
            ext.args   = '--fastqc --fastqc_args n CLIP_ARGUMENTS_HERE'
        }
}

Keep in mind that the rest of the arguments in

ext.args

will be overwritten so that is why you will need to add them where I put

CLIP_ARGUMENTS_HERE

Ah, I see, makes sense. Thanks very much Jose!