Release 1.3.0

[d4straub]

Changes in release 1.3.0 are:

• nf-core template update
• addition of --filtering_tool bbmap as alternative filtering tool option
• added peer-reviewed paper as pipeline citation
• updated nf-core modules

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/detaxizer 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).

[d4straub]

Conda fails with

   > Creating env using conda: conda-forge::sed=4.8 conda-forge::tar=1.34 [cache /home/runner/_work/detaxizer/detaxizer/~/tests/3212aafeb11ad6c327f817d3c166d3bf/work/conda/env-49d15df8f4e9927848deb1872ed78811]
   > Creating env using conda: conda-forge::python=3.12.0 numpy=1.26.3 dnaio=1.2.2 [cache /home/runner/_work/detaxizer/detaxizer/~/tests/3212aafeb11ad6c327f817d3c166d3bf/work/conda/env-233255fe9efd9760f9ee230cc961a7e4]
   > ERROR ~ Error executing process > 'NFCORE_DETAXIZER:KRAKEN2PREPARATION (1)'
   > 
   > Caused by:
   >   Failed to create Conda environment
   >     command: conda create --mkdir --yes --quiet --prefix /home/runner/_work/detaxizer/detaxizer/~/tests/3212aafeb11ad6c327f817d3c166d3bf/work/conda/env-49d15df8f4e9927848deb1872ed78811 -c conda-forge -c bioconda conda-forge::sed=4.8 conda-forge::tar=1.34
   >     status : 2
   >     message:
   >       usage: conda [-h] [-v] [--no-plugins] [-V] COMMAND ...
   >       conda: error: unrecognized arguments: --mkdir

however I cannot reproduce it. For me it works on my laptop...

[jfy133]

A few minor things otherwise very clean!

[mapo9]

lgtm 🚀

[d4straub]

Thanks!!