Number of cores calculation for Trimgalore

Description of the bug

As discussed in this issue, the calculation for actual number of cores used by Trimgalore is convoluted. The current calculation is present in this code. But, the actual core usage seems to be more than the number provided by task.cpus when the parameter --gzip is active with python3 and pigz available.

Breaking it down and drawing parallel to the comment by @FelixKrueger in the same thread, in the trimming section,

• cutadapt uses cores provided by the -j argument
• trim_galore: 1 (high)
• write to pigz stream: 1 (low)
• however, pigz would also use -j cores

This would mean, at least 2 * j + 1 cores for the trimming process.

The same would extend to the validation stage where due to pigz, the calculation would include additional j cores than the prior calculation.

Command used and terminal output

Relevant files

No response

System information

No response

Start with the linked nf-core/trimgalore main.nf calculation around line 30 and review how the trimming and validation stages account for cutadapt, trim_galore, and pigz. Done means the resource calculation reflects the additional cores used when gzip, Python 3, and pigz are active.