Metromap for Bacass

[Daniel-VM]

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/bacass 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).

PR Description

This PR includes a metro map for bacass in png, and svg format

Pending:

• Add image to README.md
• Version tag

Closes #265

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[Daniel-VM]

Fixes:

• Fix typo in liftoff module
• Reorder steps: move Genome assembly to step 2 (before taxonomic classification)
• Disconnect Kraken2 from main workflow → link directly to MultiQC
• Clarify Medaka as default path (skip shown only as opt-out via skip_polish)
• Fix annotation step: reflect all 4 tools (Prokka, Bakta, DFAST, Liftoff)
• Simplify QUAST representation (review if merging “QUAST” and “QUAST by refseq” makes sense)
• Merge MultiQC and MultiQC custom into a single output

[d4straub]

Looks great to me!

Just one small point: the figure is quite wide and the font a little small to me. Either making the font bigger or the figure less wide (for example by squeezing it horizontally) might help. I dont feel particularly strong about it though.

[Daniel-VM]

Thanks! I’ve updated the metro maps by compressing them horizontally, as the font is already set to 20px