v1.0.1

What's Changed

• chore: Update rspr to latest version by @jvfe in #178
• chore: Update rSPR image to 1.3.3 by @jvfe in #179
• feat: Add light profile to config by @jvfe in #180
• docs: Add tab for known ARETE issues by @jvfe in #181
• refactor: Remove old unused nf-core functions by @jvfe in #182
• refactor: Add rspr and evolccm to annotation entry by @jvfe in #183
• refactor: Add 1.0 threshold to subsetting heatmap by @jvfe in #184
• refactor: Optimize rspr calls and improve visualizations by @jvfe in #185
• chore: Update evolCCM image with patch by @jvfe in #187
• refactor: Change subsetting logic and move to script by @jvfe in #186
• chore: Bump ppanggolin version by @jvfe in #188
• feat(rspr): Save cluster tree in newick format by @jvfe in #189
• refactor: Save cluster tree with cluster prob by @jvfe in #190
• fix: Run rSPR when tree has duplicated nodes by @jvfe in #191
• fix: Compress output file in EvolCCM by @jvfe in #192
• fix: Avoid file location issue with ppanggolin/poppunk by @jvfe in #193

Full Changelog: 1.0...v1.0.1

v1.0

v1.0 - November 30, 2023

Added

• Automate phylogenomic analysis from ppanggolin outputs (d78dfc9)
• Add parameter to skip pangenomics/phylogenomics subworkflow (3f3f5b2)
• Add new ARETE logo (4a3b492)
• Added --annotation_tools parameter (2cf57a3)
• Validate sample IDs in annotation input check (09400c0)
• General improvements to documentation (3bdea30, 21b853b, a109c3c, a10f7bd)
• Add phylogenomics entry (1cb6563)
• Add recombination subworkflow (1d10d96)
• Add QC assembly filtering (ccc2f50)
• Improve MultiQC reports (b097f9b)
• Add rSPR (b0d0cf1, 7e494ab)
• Add entries for EvolCCM and recombination (8bdad86, 710ba25)
• Add Gene Order (6b7e268, b22988b)

Fixed

• Stop ppaggoolin from altering input file (53cbe77)
• Return PopPUNK create db outputs (339620c)
• Fix large dataset error on rSPR entry (9a119b4)

Deprecated

• No longer includes phispy information in the annotation report (82bb3f8)

v0.9

v0.9 - June 6, 2023

Added

• Make subsampling outputs only be used in Phylogenomics subwf (71240fd)
• Add gml2gv module (4775118)
• Add entry suggestion (47e4f85)
• Create concatenated outputs for annotation steps (a15cb80)
• Add genome similarity heatmap (1dfa297)
• Add pident and qcover filtering (e289b5c)
• Run RGI on Bakta outputs (de88f6f)
• Add report with annotation outputs (3c96481)
• Add ppanggolin (1409df6)
• Add presence/absence table (1e43d50)
• Add PhiSpy (080d88c)

Fixed

• Make CheckM detect file extensions (4f20672)
• Make poppunk flag only be checked at relevant points (290df03)
• Change assembly samplesheet message (893c5ac)
• Use panaroo samplesheet (4bcd833)

Deprecated

• Removed VIBRANT (080d88c)

v2.0dev

v2.0 dev - April 5, 2023

Added

• Adds stubs to every process (2a990d4)

• Adds assembly as a subworkflow (9e6d267)

• Adds dbcache (50193b3)

• Updates documentation

  • README, ROADMAP, CITATIONS, docs/usage.md, docs/output.md

• Adds test data (c57297a)

• Reorganizes output directories by subworkflow (ff53e97)

• Adds option to skip Kraken2 (192ab29)

• Adds unit tests to ARETE (6a10be0)

• Adds CI (49eb292)

• Adds initialization script to the workflow (300f524)

• Make FastTree the default under the Phylo subwf (b3a3ffa)

• Adds light parameter to the workflow (b3a3ffa)

• Concatenate and filter alignment results (8e738ef)

• Adds PopPUNK (d4ea29e)

• Updates and improves Bakta, making it the default(3cb354c)

• Adds DIAMOND alignment against ICEberg2 (ed548cb)

• Adds IslandPath (0c2ba57)

• Adds VIBRANT (f0b1f99)

• Adds Integron Finder (00735d1)

• Adds Genome subsampling using PopPUNK distances (af41029)

Fixed

• Makes assembly and assemblyqc entries available (4fd4843)
• Change databases to value channels so they can be recycled (1285c05)
• Adds missing params to config and schema (a2c2ea7)
• Integrate phylo subworkflow to the main pipeline (069400d)

Deprecated

• Removed roary (786c69c)
• Removed orthofinder (8ce706a)