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Update bclconvert module from 4.4.6 to 4.5.4 ->...
# demultiplex
m
Update bclconvert module from 4.4.6 to 4.5.4 -> https://github.com/nf-core/demultiplex/pull/409 🙏
👍🏻 2
Now that I have this done, I am interested in making a release. I really needed this new version of bclconvert. Is there anything else we would want to include?
s
Oh, I had some issue with multiqcsav the other week, let me remind myself what the issue was
I was demultiplexing two flowcells in one run, and multiqcsav gave me
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Process `NFCORE_DEMULTIPLEX:DEMULTIPLEX:BCL_DEMULTIPLEX:MULTIQCSAV` input file name collision -- There are multiple input files for each of the following file names: RunCompletionStatus.xml, RunParameters.xml, RunInfo.xml
m
oh yeah, I am unsure that multiqcsav can handle that
cc @Matthias De Smet could you confirm?
or do we just need to stage properly
m
🤔 AFAIK there should be some creative 
join
where every flowcell has it’s own SAV report. There’s no support for multiple flowcell in MQC_SAV
Might be an edgecase I overlooked when making the subworkflow
s
I used 
FOO_1
and 
FOO_2
, and it errored.
m
@Simon Pearce @Matthias De Smet any update on this?
nod 1
s
is that you have looked at it Matthias?
m
Sorry, on mobile. I didn't look at it.
s
I'll take a quick look now
m
I am interested in making a release, since we do plan to use this pipeline in our setup, but we do need this new bclconvert version, so while we're at it, we might have as well be fixing any other lingering issues that is pestering us
s
I ran with FOO_1 and FOO_2 and it worked fine 🤷
(on a smaller dataset
m
confused dog
s
So I don't know
but what I do think we should do is only publish the trimmed fastqs if we run fastp
currently it publishes all the raw fastq files, and also the trimmed ones
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