Integrate multiqcsav into bcl_demultiplex subworkflow

[delfiterradas]

Based on #9883
Closes nf-core/demultiplex#360

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[delfiterradas]

Right now multiqcsav works with bclconvert, but it is not working when using bcl2fastq

[delfiterradas]

Hi @matthdsm, I am trying to include the multiqcsav module in the bcl_demultiplex subworkflow based on the PR you had started. When using bclconvert, mutiqcsav runs successfully. However, when using bcl2fastq I get an error saying that I need to provide the RunParameters.xml file (which is not created by neither of the modules but seems still seems to work for bclconvert). Do you know if this is expected to be happening?

[matthdsm]

Hi @delfiterradas,

You can just feed all of the xml files from the run into multiqc_sav, that should fix your issue

[matthdsm]

I just checked and the bcl2fastq doesn't output any xml files, so you're going to have to patch that module first