quantms release 1.3.0

[ypriverol]

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/quantms branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile 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).

[ypriverol]

@fabianegli @jpfeuffer do you remember how to fix the error when building the PR for release, that the version do not match the comments:

╭─ [✗] 1 Pipeline Test Failed ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                                                                                                                                                                                                                 │
│ multiqc_config: 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.                                                                                                                                       │
│ The expected comment is:                                                                                                                                                                                                        │
│ This report has been generated by the <a href="https://github.com/nf-core/quantms/releases/tag/1.3.0" target="_blank">nf-core/quantms</a> analysis pipeline. For information about how to interpret these results, please see   │
│ the <a href="https://nf-co.re/quantms/1.3.0/docs/output" target="_blank">documentation</a>.                                                                                                                                     │
│ The current comment is:                                                                                                                                                                                                         │
│ This report has been generated by the <a href="https://github.com/nf-core/quantms/tree/dev" target="_blank">nf-core/quantms</a> analysis pipeline. For information about how to interpret these results, please see the <a      │
│ href="https://nf-co.re/quantms/dev/docs/output" target="_blank">documentation</a>.      

[mashehu]

@fabianegli @jpfeuffer do you remember how to fix the error when building the PR for release, that the version do not match the comments:

╭─ [✗] 1 Pipeline Test Failed ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                                                                                                                                                                                                                 │
│ multiqc_config: 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.                                                                                                                                       │
│ The expected comment is:                                                                                                                                                                                                        │
│ This report has been generated by the <a href="https://github.com/nf-core/quantms/releases/tag/1.3.0" target="_blank">nf-core/quantms</a> analysis pipeline. For information about how to interpret these results, please see   │
│ the <a href="https://nf-co.re/quantms/1.3.0/docs/output" target="_blank">documentation</a>.                                                                                                                                     │
│ The current comment is:                                                                                                                                                                                                         │
│ This report has been generated by the <a href="https://github.com/nf-core/quantms/tree/dev" target="_blank">nf-core/quantms</a> analysis pipeline. For information about how to interpret these results, please see the <a      │
│ href="https://nf-co.re/quantms/dev/docs/output" target="_blank">documentation</a>.      

did you run nf-core bump-version 1.3.0?

[ypriverol]

@fabianegli @jpfeuffer do you remember how to fix the error when building the PR for release, that the version do not match the comments:

╭─ [✗] 1 Pipeline Test Failed ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                                                                                                                                                                                                                 │
│ multiqc_config: 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.                                                                                                                                       │
│ The expected comment is:                                                                                                                                                                                                        │
│ This report has been generated by the <a href="https://github.com/nf-core/quantms/releases/tag/1.3.0" target="_blank">nf-core/quantms</a> analysis pipeline. For information about how to interpret these results, please see   │
│ the <a href="https://nf-co.re/quantms/1.3.0/docs/output" target="_blank">documentation</a>.                                                                                                                                     │
│ The current comment is:                                                                                                                                                                                                         │
│ This report has been generated by the <a href="https://github.com/nf-core/quantms/tree/dev" target="_blank">nf-core/quantms</a> analysis pipeline. For information about how to interpret these results, please see the <a      │
│ href="https://nf-co.re/quantms/dev/docs/output" target="_blank">documentation</a>.      

did you run nf-core bump-version 1.3.0?

I did it manually.

[mirpedrol]

@nf-core-bot fix linting

[mashehu]

The readme still links to an external documentation for this pipeline: https://nf-co.re/crisprseq/2.1.1/docs/usage

The website allows now multiple markdown files for usage and output documentation. See https://nf-co.re/crisprseq/2.1.1/docs/usage for example.

[ypriverol]

https://nf-co.re/crisprseq/2.1.1/docs/usage

@mashehu I can't find that URL or mention of crisprseq in our README.md can you point me to the line.

[mashehu]

I meant the links to the documentation on readthedocs, here and here.

The link to crisprseq was meant as an example on how you should do it instead.

[ypriverol]

@mashehu We have for the pipeline a lot of documentation including explanations about the topics and mass spectrometry, figures, etc is not only about the usage.

[mashehu]

I don't see why this can't be on the website (gives the material also better discoverability on search engines). If it is needed/helps to understand how to use/interpret the pipeline, it should be on nf-co.re. We have pipelines like taxprofiler with extensive documentation. It also points to the wrong repository in the installation steps there (nextflow run bigbio/quantms instead of nextflow run nf-core/quantms).