MultiQC report not triggered by FastQC input

[ktrappe]

Description of the bug

I use Nanoseq only for QC purpose, so Nanoseq only executes FastQC, NanoPlot and - given a reference - minimap2. The FastQC results however are missing in the MultiQC report. I assume Nanoseq does not recognise the FastQC input for MultiQC.

Command used and terminal output

nextflow run /pathto/nanoseq/nf-core-nanoseq-dev/workflow/ -profile rki_singularity,rki_slurm \
-w $DIR/work \
-c /pathto/profile.config \
--input $DIR/${RUNID}_samplesheet.csv --protocol cDNA \
--multiqc_title "${RUNID}_nanoseq" \
--skip_demultiplexing --skip_fusion_analysis --skip_quantification -resume

Relevant files

No response

System information

Nextflow: 22.10.6.5843
Hardware+Executor: linux HPC+slurm
Container engine: singularity
Version of nf-core/nanoseq: 3.1.0,dev

[tamuanand]

I am also facing the same issue. If I have a samplesheet with 4 or 6 samples, FASTQC.zip file of only 1 sample makes it to the MultiQC working/staging directory.

As a quick hack, I just copy over the remaining fastqc.zip files to the MultiQC work directory and re-run the multiqc command from .command.sh

I think this should fix it

Change https://github.com/nf-core/nanoseq/blob/master/workflows/nanoseq.nf#L438 from

ch_fastqc_multiqc.ifEmpty([]),

to

ch_fastqc_multiqc.collect().ifEmpty([]),