Hi, this is the updated metromap for sammyseq. Does it look good to you?

Looks nice! Small nitpicky things: • add a legend, explaining the different node symbols. What does the dashed line mean. • The dashed line doesn't look complete straight before the turn. And it seems to start a bit after the node. • It is a bit easier to quickly identify outputs by not having them exit in a straight line but be basically mirrored input lines, so their directionality is clear. • The distribution of the first few nodes is a bit chaotic. E.g. Fastqc is a bit too far to the left. I would make it equidistant between the merging joint of the two inputs and the next node. • The paths to and from the alternative nodes feel a bit compressed. Try to give them a bit more space between the on and off ramp.

Agree with Matthias • I would move the logo or the

Stage

legend to the top to give you more space too (logo + legend is cramped next to the section 3 atm) • You could also spread your input samplesheet/samples nodes so they are align with the trimmomatic/bowtie2 nodes (so they are all in line), which might add a little more consistency • The bends when you split after samtools (to boxes 2/3) are not equal

Hey, thanks a lot for the feedback! I'll try to incorporate these suggestions and send around an updated image once I’ve made the changes. Just to clarify one small point in advance we weren’t originally planning to include a legend for the solid vs dashed lines, since the dashed one represents a WIP feature that we haven't implemented yet, but which is part of the original pipeline’s analysis.

Lines and alignment are looking much better! I don't particuarly like the angled labels though, it feels a bit jarring to me (as not allt he labels are, e.g. the files). I don't think it is necessary either. You definitely need a legend for the dashed lines, because that is not intuitive what the means - when you say completed later, do you mean before release?

Thank you so much, I completely agree with everything you said! The dashed part refers to an optional, secondary analysis (box n°3), which currently stops at the SPP module. At the moment, this part is handled with local R scripts, and we plan to be port them into the pipeline. It’s not an immediate priority, but it’s definitely something we plan to complete in the future to make the pipeline more comprehensive I’ve added a legend for the dashed lines, as suggested. I’ve also aligned the file icons to the center of the main (green) line. Lastly, I made the file icons bigger where possible to improve readability. Here is the map updated