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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.
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
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
and1-ADN13260_1-lane1
should both be named1-ADN13260_1
and that1-ADN13260_1.1-ADN13260_1-lane1_1
should simply beADN13260_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
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