Wrong sample names in multiqc general table

[LouisLeNezet]

Description of the bug

Hi, When using sarek for the mapping steps the names in the multiqc general statistics table are a bit strange In the image above I think that 1-ADN13260_1.md and 1-ADN13260_1-lane1 should both be named 1-ADN13260_1 and that 1-ADN13260_1.1-ADN13260_1-lane1_1 should simply be ADN13260_1-lane1_1.

Command used and terminal output

nextflow run nf-core/sarek -profile singularity -r 3.4.4 --step "mapping" --skip_tools : "mosdepth,baserecalibrator" --outdir results --input file.csv

Relevant files

No response

System information

No response

[asp8200]

Could you share your file.csv with us?

[LouisLeNezet]

The file just looked like:

patient,sample,lane,fastq_1,fastq_2
14123,1-ADN13364_1,lane1,R1.fastq.gz,R2.fastq.gz

[FriederikeHanssen]

Hey! This is because the md files are spanning all input files belonging to a single sample. The Read QC on the other hand are computed for each fastq file separately. This should be massively simplified with the latest MultiQC release that allows grouping of QC stats that are split over several files. WE just need to add Fastp support for this in MultiQC itself