`getTrimGaloreReadsAfterFiltering` function fails to extract filtered read count from TrimGalore log

[iraiosub]

Description of the bug

The getTrimGaloreReadsAfterFiltering function in the FASTQ_FASTQC_UMITOOLS_TRIMGALORE subworkflow incorrectly parses TrimGalore log files, leading to misleading read count reporting. See issue nf-core/modules#8576

Problem: The regex pattern expected exactly one standard space after the colon when extracting filtered read counts, but TrimGalore logs can contain tabs or multiple/non-standard spaces. This caused the regex to fail silently, returning the total number of reads processed instead of reads that passed filtering. This is reflected in the multiQC Cutadapt section.

Impact on Pipeline:

• Incorrect read count reporting – Users may see misleading numbers for reads retained after trimming
• Silent failure – No error thrown, making the issue hard to detect

Solution

Updated the regex pattern from requiring exactly one space to allowing any amount/type of whitespace directly in the FASTQ_FASTQC_UMITOOLS_TRIMGALORE subworkflow. See PR nf-core/modules#8577

Command used and terminal output

nextflow run nf-core/rnaseq -r 3.18.0 \
--input 'samplesheet.csv' \
--fasta $REFDIR/GRCh38.primary_assembly.genome.fa \
--gtf $REFDIR/gencode.v44.primary_assembly.annotation.gtf \
--gencode \
--remove_ribo_rna \
--with_umi \
--umitools_bc_pattern NNNNN \
--extra_trimgalore_args "--clip_R1 3 -a A{11}" \
--extra_salmon_quant_args="--noLengthCorrection" \
-resume \
-profile singularity,crick

Relevant files

h0_C_2_trimmed.fastq.gz_trimming_report.txt

System information

Nextflow v24.10.2
HPC
slurm
Singularity v3.11.3

[pinin4fjords]

Thanks! Will pull that fix in before release

[pmoris]

Where is this filtered read count used or logged by the pipeline btw?

Just asking because this reminded me of an earlier discussion we had regarding the number of filtered too short reads that was reported by multiQC (FelixKrueger/TrimGalore#200 & MultiQC/MultiQC#1557 (comment)).