chore: re-label process_low to fastqc#9814
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SPPearce merged 2 commits intonf-core:masterfrom Feb 3, 2026
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Can you do the same test for FALCO? As that is a newer reimplementation. |
SPPearce
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I can do it but I prefer each module in a specific branch. I will create later if I found the similar issue. |
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Yes, I wasn't suggesting to do it as part of this PR. |
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PR checklist
Closes #XXX
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile condaDescription:
After benchmarking FastQC with different thread settings, it appears that FastQC does not follow the modern parallelization model where increasing the number of threads for a single dataset reduces runtime. Instead, its threading model is closer to a GNU parallel wrapper: users are expected to set the number of threads to match the number of FastQC input files, allowing multiple files to be processed in parallel.
In practice, however, FastQC rarely processes more than two FASTQ files at the same time in typical pipelines. As a result, for paired-end samples (two FASTQ files) or single-end samples, using a low-resource configuration (e.g. process_low) is sufficient and does not impact overall runtime. FastQC is using in many pipeline for quality control, while using
process_lowis wasting resource.Quick benchmark result: Using the same dataset, increasing cpus and memory does not help at all.

For details, follow this blog:
https://riverxdata.github.io/river-docs/blog/bioinformatics-computing-resource-optimization-part1