Update metromap and logo

[LouisLeNezet]

Update the main metro map and add the different version of the pipeline logo with the dog symbol.

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/phaseimpute branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[atrigila]

Thanks for addressing this. Here is some feedback: It is not clear what the meaning of the different color routes mean. They seem to represent different files, but they normally should represent methods (see rnaseq, sarek or taxprofiler). There is also no need to clarify in a legend if something is a module/subworkflow since the diagram is already too simplified. I do see a value in clarifying which are mandatory/optional (see sarek as an example).

[LouisLeNezet]

The colors effectively represent the samplesheet the user will give (--panel, --input, --chunks, --posfile, --input-truth)
Which coloring pattern would you use ?
The issue is that if use the same color everywhere this would be a bit bland.
I will send you a proposition by slack.

[atrigila]

I understand you added a legend for the colours. I think you want to keep the colours for an aesthetic reason but I do not think they follow the same pattern as all nf-core pipelines.

I don’t think there is any issue in keeping a simple colour schema. It doesn’t have to have plenty of colours if it doesn’t need to.

If you really want to use colours, one possibility would be to color paths according to the step. For example all lines to outputs in panelprep are one colour (instead of having orange, red and blue, they can be all orange). Then the lines that are inputs to imputation are another colour (now they are red, blue, orange, green, they could be all green). Then the input to validate another colours (now green and yellow, they could be all yellow). Same with simulate (now green, it can be kept green / or any different colour to the other steps).

This way, you would keep the colours but respect the “functionality” of how colour tubes are used in other nf-core pipelines.