Pipeline Release Version 1.1.0

[DSchreyer]

v1.1 - [2024-01-30]

Credits

Special thanks to the following for their input and contributions to the release:

• Jens Luebeck
• Simon Pearce
• Maxime U Garcia
• Alex M. Ascensión

Enhancements & fixes

• Nf-core template update to 2.11.1
  • update of nf-core modules versions
• Removed AmpliconArchitect and AmpliconClassifier modules with their respective scripts in /bin
  • AmpliconArchitect and AmpliconClassifier is now run inside the AmpliconSuite-Pipeline. Additional scripts are not necessary.
  • Removed respective configs and workflow code
• Added AmpliconSuite-Pipeline
  • A wrapper for calling copy numbers, preparing amplified intervals, running AmpliconArchitect, and calling amplicon classes using AmpliconClassifier
  • Added docker container named PrepareAA to run AmpliconSuite-Pipeline with singualarity or docker
  • Added module configs and description
• Changed assets/multiqc_config.ymlto fit new pipeline version
• Included directory checks for mosek_license_dir and aa_data_repo .
  • Removed both directory parameters in the test profile as it is only checked when running ampliconarchitect
• Updated nextflow_schema.json to give better details about how to use --circle_identifier
• made --circle_identifier an essential parameter
• made --input_format an essential parameter
• Updated --bwa_index to accept only directory paths to the bwa index files. Makes the user input easier to not need to deal with file endings and patterns. Bug identified by Alex M. Ascensión in --bwa_index: string [database/indexes/GRCm38/BWA/genome.bwt] does not match pattern ^\S+\.\{amb,ann,bwt,pac,sa\}$ (database/indexes/GRCm38/BWA/genome.bwt) #68

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/circdna 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).

[SPPearce]

MultiQC is now a local module, except this meta file which is still here.
Why is it now a local module, what has changed?

[SPPearce]

Suggested change

	## v1.1 - [2024-01-30]
	## v1.1 - [2024-02-01]

[SPPearce]

Just a minor point about the multiqc file still in modules/nf-core.
If you are slightly changing the multiqc module from the one in the modules repo, you can use a patch file rather than moving it into local.