arete - v1.0.1

What's Changed

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

Full Changelog: https://github.com/beiko-lab/arete/compare/1.0...v1.0.1

- Python
Published by jvfe about 2 years ago

arete - v1.0

v1.0 - November 30, 2023

Added

• Automate phylogenomic analysis from ppanggolin outputs (d78dfc9d811bac6f8f0f5d0d71cb31a24dadaf02)
• Add parameter to skip pangenomics/phylogenomics subworkflow (3f3f5b218e94adb6ba6d743e3b8854bebae02eb4)
• Add new ARETE logo (4a3b49275d124ca92186d9e82ea2e700bfbf1f2f)
• Added --annotation_tools parameter (2cf57a3a06be53d0550a004101d199fc1760f84d)
• Validate sample IDs in annotation input check (09400c0e10919001286c8e829299c03129dd64c2)
• General improvements to documentation (3bdea3083d9dfc3f23a198a23843820ac68be2ca, 21b853bf065da239247ed62a2a670f2d25a56de, a109c3c19576cffa9a1029e58229c3054806a017, a10f7bd4ff73bcadb389d18a82d18c6508792237)
• Add phylogenomics entry (1cb656372a752bb9288b3e220cbddc71943d4496)
• Add recombination subworkflow (1d10d96612c7c7e7f0a7c703771b1ce7d76b35a9)
• Add QC assembly filtering (ccc2f50c7342bb05598cf8deb64cab332acbcfdb)
• Improve MultiQC reports (b097f9b58722d7ff99a1bb4c057152f4e0875dca)
• Add rSPR (b0d0cf1467c7f86aa01e023b359e0fe31e7029ad, 7e494ab18d3bcff2e9da87af103c9b2ebe164b20)
• Add entries for EvolCCM and recombination (8bdad860fd75f6d1b06034201874f4739a20895f, 710ba2524f7850938039d6dd4703b47065d49768)
• Add Gene Order (6b7e2685143db2d1153ce8cd58b0baab84b064dc, b22988b7a0b945c63f8261fb27dc4b6ccc0f64b0)

Fixed

• Stop ppaggoolin from altering input file (53cbe771c8af23432cfec09b95be7ac6a27c3d0d)
• Return PopPUNK create db outputs (339620c9257e7d99c8b5f933f298e3b2f3e96b14)
• Fix large dataset error on rSPR entry (9a119b4fa588707e36114d864a0ad4cc38cc239c)

Deprecated

• No longer includes phispy information in the annotation report (82bb3f8069a714cd423bef8bdd9e03b2f0f8f919)

- Python
Published by jvfe over 2 years ago

arete - v0.9

v0.9 - June 6, 2023

Added

• Make subsampling outputs only be used in Phylogenomics subwf (71240fdf1db73991e9e0ae74cacce3b1007d324b)
• Add gml2gv module (4775118f113e38741852a718304241bfdb57cb60)
• Add entry suggestion (47e4f8589c5cc2370033e6f18b9da6251193cb5b)
• Create concatenated outputs for annotation steps (a15cb80a79311f6ba7a860cc8f716a6f61df1610)
• Add genome similarity heatmap (1dfa297a1c6236f30d83e884bcc5f2426d7cba07)
• Add pident and qcover filtering (e289b5caa624f98e1bcde2ac7d105237ce81c7a2)
• Run RGI on Bakta outputs (de88f6f574b6786eb47bba237894d50baba9886d)
• Add report with annotation outputs (3c96481090a0785fbc280a6818be05df2ab33000)
• Add ppanggolin (1409df676e9c964c972132f8466840a75b5981d9)
• Add presence/absence table (1e43d5032eb026877f18e800ea16bfc8b0821c9d)
• Add PhiSpy (080d88cde7cd05e12e40fa1703f4ab77f28e071f)

Fixed

• Make CheckM detect file extensions (4f2067263f84959f96a203e1b18d1d0832d2efa4)
• Make poppunk flag only be checked at relevant points (290df03b07479ec20c077bfc926aadb860aaa96d)
• Change assembly samplesheet message (893c5ace3755e43efafd6ecc075194a7c4eeb614)
• Use panaroo samplesheet (4bcd83371c32ef93be9604c3de116bf4d0867df0)

Deprecated

• Removed VIBRANT (080d88cde7cd05e12e40fa1703f4ab77f28e071f)

- Python
Published by jvfe about 3 years ago

arete - v2.0dev

v2.0 dev - April 5, 2023

Added

• Adds stubs to every process (2a990d48d1d024)
• Adds assembly as a subworkflow (9e6d2679242)
• Adds dbcache (50193b35)
• Updates documentation
  • README, ROADMAP, CITATIONS, docs/usage.md, docs/output.md

• Adds test data (c57297ad922)

• Reorganizes output directories by subworkflow (ff53e97129effb)

• Adds option to skip Kraken2 (192ab2918997bb0d35d2195b8d3da)

• Adds unit tests to ARETE (6a10be029268eb2f1d526913a8022a)

• Adds CI (49eb2929f287643446c5eb073670435e45a559a9)

• Adds initialization script to the workflow (300f52429ee9cee5e056)

• Make FastTree the default under the Phylo subwf (b3a3ffa0e64367)

• Adds light parameter to the workflow (b3a3ffa0e64367)

• Concatenate and filter alignment results (8e738ef237bcc80b6d9)

• Adds PopPUNK (d4ea29eaaad54905a81ca5a0c31a699c9ff89b2)

• Updates and improves Bakta, making it the default(3cb354c9c6e20346e6a844e9a0c55060fb8dff)

• Adds DIAMOND alignment against ICEberg2 (ed548cb8ac8bf44d68b)

• Adds IslandPath (0c2ba57999f4952e1eb1db3b3107a4ccbdc5ad86)

• Adds VIBRANT (f0b1f99a2c7ded75e6684e8775e052ca2ec6e140)

• Adds Integron Finder (00735d15aa5d6fef67793fd32152ea91cfa65c2a)

• Adds Genome subsampling using PopPUNK distances (af41029c9ce6d2308f3)

Fixed

• Makes assembly and assemblyqc entries available (4fd48439be9)
• Change databases to value channels so they can be recycled (1285c0582b5f78)
• Adds missing params to config and schema (a2c2ea7d216b15f3652)
• Integrate phylo subworkflow to the main pipeline (069400dde1d098fe)

Deprecated

• Removed roary (786c69c223261846)
• Removed orthofinder (8ce706a7a040d0)

- Python
Published by jvfe about 3 years ago