wrong link to global report in MultiQC

[fbnrst]

Description of the bug

I just finished my first seqinspector run, very helpful tool, thanks!

I found a small bug, not sure, whether it belongs here or into MultiQC:

In the MultiQC report, there is a section "nf-core/seqinspector MultiQC Reports Index"

The links to the groups work perfectly, but the link to the global report is off.

As an example I paste a few lines from multiqc/global_report/seqinspector_multiqc_report.html:

The

<div class="list-group">
  <a href="../global_report/multiqc_report.html" target="_blank" class="list-group-item list-group-item-action">Global report</a>
  <a href="../group_reports/batch1/multiqc_report.html" target="_blank" class="list-group-item list-group-item-action">Group report: batch1</a>
  <a href="../group_reports/batch2/multiqc_report.html" target="_blank" class="list-group-item list-group-item-action">Group report: batch2</a>
</div>

The issue is that the link of the global reports points to multiqc_report.html, but the filename for me is seqinspector_multiqc_report.html.

Command used and terminal output

Relevant files

No response

System information

No response

[pontushojer]

Hi @fbnrst which version of seqinspector are you running? The global report should be multiqc/global_report/multiqc_report.html so I am not sure where the seqinspector_ prefix is coming from in your run. Running dev I get the correct path and its also correct for version 1.1.0 based on the test run (https://nf-co.re/seqinspector/1.1.0/results/seqinspector/results-9d2c6933af916df5dba430e5600ae733804bf1fe/multiqc/global_report/). Are you running any custom configurations that might modify the file names? Would you be able to share you run log and config files?

[fbnrst]

Thanks for the quick answer!

I used version 1.1.0, executed the run like

NXF_CACHE_DIR="../../.nextflow/cache/nf-core_seqinspector" pixi run -e nextflow26 \
    nextflow \
    -log "../../.nextflow/log/nf-core_seqinspector" \
    run nf-core/seqinspector \
    -work-dir "../../.nextflow/work/nf-core_seqinspector" \
    -c "korok.config" \
    -params-file params.yml \
    -r 1.1.0 \
    -resume

where I have a pixi environemt that has nextflow installed.
And here is my params.yml:

input: ../../intermediate_data/samplesheet/samplesheet_seqinspector.csv
outdir: ../../intermediate_data/nf-core_seqinspector
tools: fastqscreen,fq_lint,seqfu_stats
tools_bundle: null
fastq_screen_references: ../../intermediate_data/samplesheet/fastq_screen_references.csv
multiqc_title: "seqinspector"
email: ***

And the issue then probably stems from the multiqc_title: "seqinspector" option, because this matches the multiqc filename change.

[pontushojer]

Thank you for the info! Setting the parameter --multiqc_title to "seqinspector" did indeed change the report name to seqinspector_multiqc_report.html.

It seems that modifying the MultiQC report title also changes the output file name https://github.com/MultiQC/MultiQC/blob/14f071465794fdfb4392e2038d073a35e8524ad7/multiqc/multiqc.py#L190 . We need to set a static output name for the global report or change the output block specs similar to what we do for the group reports (that maintain the correct name) here:

seqinspector/main.nf

Line 171 in 00d5b69

file >> "multiqc/group_reports/${meta.id}/multiqc_report.html"

So for now, skip the multiqc_title parameter if you want the "Report index" section to work as intended.