Release - 1.1.0

[jannikseidelQBiC]

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 lint).
• 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).

This PR was made against the master branch to release version 1.1.0 of detaxizer. Changes see below.

PR 33 - Bugfix in parse_kraken2report.nf

• Addition of quotation marks in parse_kraken2report.nf prevents failure of the pipeline when using a taxon with space (e.g. Homo sapiens) with the tax2filter parameter

PR 34

Improving detaxizer by making the workflow more modular and enabling bbduk as second tool for classification. Also turning off blastn validation by default (too resource intensive for a default setting). Further smaller improvements see below.

Introduction of bbduk into the classification step

• To increase the capabilities of detaxizer bbduk was introduced
• The summary step was adapted to this change

Making blastn optional

• blastn is now optional as it is very resource intensive (especially in terms of time) when many reads are classified

Making fastp optional

• fastp removed duplicates from the files by default, which were then not part of the classification step and therefore not filtered (except if the filter_trimmed parameter was used)
• the removal of duplicates can be turned on by setting fastp_eval_duplication

Output of removed reads

• If the filter is used, then one can now optionally give out the removed reads in separate files using the output_removed_reads flag

Optional classification

• Filtered and removed reads can now be optionally classified by kraken2 using the classification_kraken2_post_filtering flag

PR 39

Added generation of samplesheet for MAG, Taxprofiler by @Joon-Klaps

PR 42

Template update for nf-core/tools v3.0.2

[jannikseidelQBiC]

The failing test is due to the master branch not having this in the download_pipeline.yaml and the pipeline not supporting stub run. This is fixed in this version.

[jfy133]

Despite my many comments, I do not see any blockers here :)

[jfy133]

GTG now @jannikseidel !