MultiQC is not consolidating QUAST reports for assemblies

[amizeranschi]

Hi,

As the title mentions, with more recent versions of the pipeline (tested with 3.2.1 and 3.3.0), it seems that MultiQC is not consolidating QUAST reports for assemblies, which used to be the case with older pipeline versions like 3.0.2.

Is this expected behavior, or is it a bug?

To reproduce:

nextflow run nf-core/mag -r 3.0.2 \
-profile docker,test \
--skip_spades \
--skip_prodigal \
--skip_prokka \
--skip_metaeuk \
--skip_binning \
--skip_gtdbtk \
--outdir test-mag-3.0.2

ls -1 test-mag-3.0.2/multiqc/multiqc_data/multiqc_quast.yaml
# test-mag-3.0.2/multiqc/multiqc_data/multiqc_quast.yaml

ls -1 test-mag-3.0.2/multiqc/multiqc_data/
# test-mag-3.0.2/multiqc/multiqc_data/multiqc.log
# test-mag-3.0.2/multiqc/multiqc_data/multiqc_Kraken2_Kraken2.yaml
# test-mag-3.0.2/multiqc/multiqc_data/multiqc_bowtie2.yaml
# test-mag-3.0.2/multiqc/multiqc_data/multiqc_citations.yaml
# test-mag-3.0.2/multiqc/multiqc_data/multiqc_data.json
# test-mag-3.0.2/multiqc/multiqc_data/multiqc_fastp.yaml
# test-mag-3.0.2/multiqc/multiqc_data/multiqc_fastqc.yaml
# test-mag-3.0.2/multiqc/multiqc_data/multiqc_fastqc_1.yaml
# test-mag-3.0.2/multiqc/multiqc_data/multiqc_general_stats.yaml
# test-mag-3.0.2/multiqc/multiqc_data/multiqc_quast.yaml
# test-mag-3.0.2/multiqc/multiqc_data/multiqc_software_versions.yaml
# test-mag-3.0.2/multiqc/multiqc_data/multiqc_sources.yaml


nextflow run nf-core/mag -r 3.3.0 \
-profile docker,test \
--skip_spades \
--skip_prodigal \
--skip_prokka \
--skip_metaeuk \
--skip_binning \
--skip_gtdbtk \
--outdir test-mag-3.3.0

ls -1 test-mag-3.3.0/multiqc/multiqc_data/multiqc_quast.yaml
# ls: cannot access 'test-mag-3.3.0/multiqc/multiqc_data/multiqc_quast.yaml': No such file or directory

ls -1 test-mag-3.3.0/multiqc/multiqc_data/
# test-mag-3.3.0/multiqc/multiqc_data/multiqc.log
# test-mag-3.3.0/multiqc/multiqc_data/multiqc_Kraken2_Kraken2.yaml
# test-mag-3.3.0/multiqc/multiqc_data/multiqc_bowtie2.yaml
# test-mag-3.3.0/multiqc/multiqc_data/multiqc_citations.yaml
# test-mag-3.3.0/multiqc/multiqc_data/multiqc_data.json
# test-mag-3.3.0/multiqc/multiqc_data/multiqc_fastp.yaml
# test-mag-3.3.0/multiqc/multiqc_data/multiqc_fastqc.yaml
# test-mag-3.3.0/multiqc/multiqc_data/multiqc_fastqc_1.yaml
# test-mag-3.3.0/multiqc/multiqc_data/multiqc_general_stats.yaml
# test-mag-3.3.0/multiqc/multiqc_data/multiqc_software_versions.yaml
# test-mag-3.3.0/multiqc/multiqc_data/multiqc_sources.yaml