Improve the pipeline workflow graphic/map

[U13bs1125]

followed the guidlines from nf-core site: https://nf-co.re/docs/guidelines/graphic_design

PR checklist

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

[charles-plessy]

Nice work, and it addresses the comments in PR #9 !

[mashehu]

nice improvement. More smaller comments if I may:

• the logo is off: the "parigenomealign" is squeezed and the apple is too close to nf-core (plus if you keep the slash from the original logo, it makes it more coherent with other nf-core logos, but this is not that important, just gives a nicer consistency over all)
• you explain the black and the blue, but not the green line.
• could you use connected dots for shared steps in the top left (see https://raw.githubusercontent.com/nf-core/taxprofiler/1.1.8//docs/images/taxprofiler_tube.png as an example). Also I would differentiate between input dots, output dots and processing dots (was looking for a label for the first dots 🙂)
• I think you can simplify the labels a bit so you don't have to repeat yourself so often especially for the results. one idea: drop the "alignment(s)" and write it as a section label to the right. group the different alignments with their corresponding dotpots, for example with using a different color for each type (again take taxprofiler's tubemap as an example)

[mashehu]

oh and one more thing: if you add the version number of the release to the map (usually next to the logo), it becomes easier to differentiate if the pipeline's functionality grows