Hey everyone! I'm working on a large sequencing project with approx 60 rnaseq samples, and each sample has multiple FASTQ files (R1/R2 and potentially multiple lanes). I'm using FastQC output followed by MultiQC to summarize quality metrics, and I would like to group all files belonging to a sample (based on the sample ID in the filename) under a single sample name without merging FASTQ files (since they are huge). I am trying to achieve the following • Use the filename as the initial sample name without MultiQC auto-cleaning it (

_R1

,

_trimmed

, etc.). • Apply a custom regex via

sample_names.replace

to extract a clean sample ID like

100113-001-001, 100113-001-002 etc.

. • Have MultiQC report grouped by sample, with all lanes/read pairs listed together (multiple rows under the same sample name). • Avoid any unexpected overwriting or collapsing of sample names due to default cleaning behavior. I tried to use the content below in a multiqc_config file, but the sample names are still the same. I appreciate any help! 😊

sample_names:
  replace:
    - pattern: ".*?(\\d{6}-\\d{3}-\\d{3}).*"
      replace: "\\1"

Are you aiming to group samples as described in this blog post? https://seqera.io/blog/multiqc-grouped-samples/

Thanks for looking into this @Phil Ewels . The grouped samples functionality is exactly what I need. Thanks!!