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32 update pipeline metro map on the readme page #36

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32 update pipeline metro map on the readme page #36

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added pipeline metromap, updated README page
khersameesh24 Nov 23, 2024
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Update README.md
khersameesh24 Nov 24, 2024
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Merge pull request #34 from khersameesh24/32-update-pipeline-metro-ma…
khersameesh24 Nov 25, 2024
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suggested changes to metro map
khersameesh24 Nov 28, 2024
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Merge pull request #39 from khersameesh24/32-update-pipeline-metro-ma…
khersameesh24 Nov 28, 2024
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6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -12,7 +12,9 @@

## Introduction

**nf-core/spatialxe** is a bioinformatics best-practice processing and quality control pipeline for Xenium data. **The pipeline is currently under developement and no completed yet!**
**nf-core/spatialxe** is a bioinformatics best-practice processing and quality control pipeline for Xenium data. **The pipeline is currently under developement and not completed yet!**. The current plan for the pipeline implementation is shown in the metromap below. Please note that the pipeline steps and methods might change as we move forward in the development cycle.

![nf-core/spatialxe-metromap](docs/images/spatialxe-metromap.png)

The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

Expand All @@ -22,8 +24,6 @@ On release, automated continuous integration tests run the pipeline on a full-si

## Pipeline summary



## Quick Start

1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`)
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please also provide an svg version. makes it easier to edit it in the future.

Looks very nice, some small nit-picking:

  • The orange and the green are the same kind of brown for red-green-sight-deficiant people.
  • try to center seggar and resegment nodes inbetwen the curves (also resegment could need some padding to the left)
  • you have enough space for cellpase and proseq to be actually next to their node.
  • try to make the gray boxes have the same distance to the green line after baysor
  • I would try to make the relabel process in the same hight as 5the coordinates/mask one, makes it easier to see that it is actually another input path.
  • speaking of input: their symbol is not expalined in the legend
  • I don't know if the arrows are actually needed. try if everything is still readable without them.
  • the folder for xenium bundle is not centered, smae with the ro-crate symbol to the right and the spatialdata icon to the left of coordinate mask. similarly, the gen epanel json icon and the html qc reports are not centeredd horizontally. and the first coorcinates/mask is neither.
  • thinking about the color usage. what if instead of approach the encode the original data. so you could use blue for transcripts and orange for morphology and drop green and just combine the two after the baysor step and thereafter

but again this are just small things the whole thing looks very clear, congrats!

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Hi @mashehu, I have made the suggested changes and updated the metromap. Also, added the svg for the metromap.

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4 changes: 4 additions & 0 deletions docs/images/spatialxe-metromap.svg
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