Modify MultiQC module results

[jfy133]

Is your feature request related to a problem? Please describe.
At the moment the MultiQC results are in reverse order, which doesn't make sense in the natural way of reading and doing quality control.

Describe the solution you'd like
Provide and/or modify the default multiqc.config file that comes with the singularity/docker/conda 'images' to reflect the
order in which each module is run.

More context is provided here: https://multiqc.info/docs/#order-of-modules

Describe alternatives you've considered
Add to documentation to read in reverse

Example

I've not tested this, but something along the lines of?:

report_comment: >
    This report has been generated by the <a href="https://github.com/nf-core/eager" target="_blank">nf-core/eager</a>
    analysis pipeline. For information about how to interpret these results, please see the
    <a href="https://github.com/nf-core/eager" target="_blank">documentation</a>.
report_section_order:
    nf-core/eager-software-versions:
        order: -1000
    fastqc:
        after: 'nf-core/eager-software-versions'
    adapterRemoval:
        after: 'fastqc'
    Samtools:
        after: 'adapterRemoval'
    dedup:
        after: 'Samtools'
    qualimap:
        after: 'dedup'
    preseq:
        after: 'qualimap'

If you agree I will try it out and then do a pull request.

[apeltzer]

Yes, this is nice - I will have to work on the required modules (e.g. adding DamageProfiler to multiqc... which is still not finished because I never find the time to do it...) but also creating custom content results such as cluster factor etc in the main table... its possible, but I'd need to have a more detailed list of required things and we should have proper and ideally complete documentation on what we would like to have in such a pipeline report table in general first :-)

[apeltzer]

Your PR was already a good start - I merged it in!

[jfy133]

When you have a moment, could you try the .yaml file above? I just tried various versions of the above but the output never seems to change?

e.g. with dev version

nextflow run nf-core/eager \
--reads 'data/ABM006.A0101/*_R{1,2}*fastq.gz' \
--pairedEnd \
--fasta 'references/hg19_MT.fasta' \
--outdir 'output_eager2' \
--max_cpus 4 \
--max_mem 32G \
-r dev

or manually with:

multiqc --config ~/.nextflow/assets/nf-core/eager/conf/multiqc_config.yaml .

[apeltzer]

Pinging @ewels here - the current configuration should actually work fine IMHO. Did we do anything wrong here?

[ewels]

Hmm, looks fine to me too. What does the verbose log say from MultiQC? Near the top it should say whether it successfully parsed your config file or not. Is the whole thing ignored, including the comment?

[apeltzer]

I'll run dev quickly and upload the log here...

[jfy133]

This is my output (including multiqc logs and the YAML file itself). It appears to find and parse the config file without any error being thrown.

multiqc_orderIssue_20181119.zip

[jfy133]

@ewels let us know if you want to raise an issue on the MultiQC repo, if you don't see anything immediately that suggests we did something silly in the error files above.

[ewels]

Probably a good idea, will try to find time to have a look over the next couple of days. @apeltzer can remind me in person :)

[jfy133]

Seems to be fixed using 'top modules' instead.