Added

• #79 - New optional reftreename sample sheet column, grouping rows that place onto the same reference tree so that the group is also grafted, classified and heat-treed as a whole, instead of only one profile at a time (#78) (by @erikrikarddaniel)
• #75 - Derive taxonomy from --refseqfile FASTA headers (GTDB single-file style) when --taxonomy is not given, instead of skipping taxonomic classification entirely (#66) (by @erikrikarddaniel)
• #72 - Alignment coordinates, lengths and coverage for each hit in the ranked hmmsearch summary, when --save_domtblout is set (#70) (by @erikrikarddaniel)
• #71 - New --save_domtblout option, saving hmmsearch’s per-domain hit table in “search and place” mode (#69) (by @erikrikarddaniel)

Fixed

• #85 - Build every conf/test*.config and tests/nextflow.config test-data URL from params.pipelines_testdata_base_path (or params.modules_testdata_base_path for the handful that live on the shared modules branch instead), instead of hardcoding the full URL, so a fork’s phyloplace branch can be tested with a single --pipelines_testdata_base_path override without also re-pointing the shared-branch files (#80) (by @erikrikarddaniel)
• #84 - Use relative links between our own docs pages again, now that a website fix means they resolve correctly, instead of absolute links that silently pointed to the released docs (#83) (by @erikrikarddaniel)
• #71 - Correct the hmmsearch output files listed in the output documentation, where the human-readable table was listed as *.tbl.gz instead of *.txt.gz (by @erikrikarddaniel)

Changed

• #88 - Change the default --alignmethod from hmmer to clustalo, except when --hmmfile is given (or filled in a samplesheet row), which still implies hmmer. Runs that relied on the previous default now align with Clustal Omega and produce clustalo/ output instead of hmmer/; pass --alignmethod hmmer to keep the old behaviour (by @erikrikarddaniel)
• #81 - Update gappa/examineassign, gappa/examinegraft and gappa/examineheattree to gappa 0.9.0, so every gappa step runs the same version and container (nf-core/modules#12858) (by @erikrikarddaniel)
• #79 - Publish grafted trees as <id>.graft.newick instead of <id>.graft.<id>.epa_result.newick, dropping a repetition of the name and matching the new joint outputs (by @erikrikarddaniel)
• #77 - Adopt typed params blocks for pipeline-specific parameters, fixing boolean options (e.g. --save_domtblout false) that couldn’t be turned off from the command line (#74) (by @erikrikarddaniel). Raises the minimum required Nextflow version to 26.04.0.
• #73 - Update seqtk/subseq and fasta_hmmsearch_rank_fastas to fix output filenames glomming the input sequence filename onto the prefix (nf-core/modules#12779) (by @erikrikarddaniel)
• #68 - Template update to 4.1.0 (by @erikrikarddaniel)

Dependencies

Thanks

Thanks to everyone who reviewed PRs along the way to this release: @piplus2, @dialvarezs, @Joon-Klaps, @danilodileo and @nschan.