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Trying to update the subway map before the coming ...
# seqinspector
m
Trying to update the subway map before the coming release. Nitpicking welcome cc @James Fellows Yates
j
Given you are going top down, I would move Run FOlder/FASTQ on top and have vertical lines going into CheckQC/FQlint etc
And I'm sorry but I cannot for the life of me work out the bottom bit
But I wonder if it's necessary at all?
(within the metromap I mean)
And I would argue to add more colour, e.g. have the FASTQ lines be one colour, and the RunFolder line as another colour
(within the metromap I mean)
I think this grouping system would be better as a different figure/plot
m
Oh, I like what you're thinking
Thanks
I'll have a go tomorrow
f
And the lower part is one of the major features of the pipeline
It might have to come with some explanations since it looks a bit complicated, but I promise you it is not complicated at all
basically what we do is to generate multiple multiqc files each including samples of a specific tag that is specified in the sample sheet
like that we can dump the fastq files of an entire flowcell with lots of different projects into the pipeline and we get individualized reports for each project as well as a global report with all of them for a Flowcell QC step.
m
I agree that it's an important part
f
we could consider to reduce the amount of tags displayed
but I would leave the part in itself
what I mean is, we could reduce the amount of tags from 7 to 3 or something, to make it less heavy
anyhow, I was not intending to open slack
have a great easter weekend
j
And the lower part is one of the major features of the pipeline
Fair enough but it doesn't really fit very well into the (my opinionated) scope of a metromap which means it is meant to be a very simple overview to get s rough idea of the steps - not the details of specific outputs. In his case I would just have lots of multiple multiqc file icons as output ,maybe with little titles (single sample; whole flow cell), to indicate the flexibility/power and put the detailed diagram of how those look in a separate figure Either that or massively simplify the diagram. It looks very nice stylistically, but I still at a glance cannot understand what it's trying to say/do - mainly the rows bit on the left. The ABCD columns I can sort of follow it I look a little bit longer
m
Haven't reworked the vertical input yet, but more colors looks good
And definitively given that runfolder info only goes towards the global multiQC report, we need that lower back part
But it can indeed be reduced
j
Oh that's nice
m
Trying out nf-metro
Advantage of using such a layout, anyone can update even with no inkscape skills
f
yeah, but it’s not quite as pretty…
m
Definitively not
j
If you go top down it will look more familiar I think
m
Can't do it yet, waiting on a new release from Jon
👍 1
j
But agree not quite as pretty
Particularly file icons
party this 1
m
I made an issue for Jon to make it nicer too 🤣
😆 1
Jon made a suggestion based on my latest attempts. What do you all think: https://seqeralabs.github.io/nf-metro/dev/pipelines/seqinspector/
m
isn't it a bit misleading saying fastq files and bam files go to multiqc, if it is just he qc logs?
m
You could give anything to mqc actually. I see your point, but given the point of this pipeline, I'd say we're ok this way. That being said, I'll try to make more subgraphs in the future
j
You could change the legend to say 'Run data' 'FASTQ data' 'BAM data' rather than files
💯 1
Because then you hinting representing the paths the contents of the files go through
m
Gotcha
j
And it distingujishes a bit more from the FASTQ file icon
My only quibble is I personally don't like end point being in the top right hand corner . If we are assuming western L->R T->D directiron, at a minimum the multiqc section should be center aligned (LR) or finishes in the bottom right
I like flow like water 😉
m
also the BBmap label should be below the nodes like the rest (actually I think if possible labels should be above the nodes, but I guess that's even more difficult)
m
Cannot figure out how to change labels position
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