### `Added` - [#718](https://github.com/nf-core/mag/pull/718) - Add support for independent long-read metagenomic assembly (requested by @ljmesi and many others, added by @muabnezor) - [#718](https://github.com/nf-core/mag/pull/718) - Added metaMDBG and (meta)Flye as long read assemblers (added by @muabnezor) - [#718](https://github.com/nf-core/mag/pull/718) - Added host removal for long reads using minimap2 as aligner (added by @muabnezor) - [#827](https://github.com/nf-core/mag/pull/827) - Added nf-test CI testing for all test profiles (added by @jfy133) - [#829](https://github.com/nf-core/mag/pull/829) - Add `--skip_shortread_qc` and `--skip_longread_qc` params for skipping certain default preprocessing steps (added by @erikrikarddaniel) - [#846](https://github.com/nf-core/mag/pull/846) - Improve documentation of `group` samplesheet column (added by @vinisalazar) - [#855](https://github.com/nf-core/mag/pull/855) - Add basic nf-tests for test_longreadonly, test_longreadonly_alternatives, test_hybrid and test_assembly_input (added by @dialvarezs) - [#864](https://github.com/nf-core/mag/pull/864) - Add `--gtdbtk_skip_aniscreen` to disable fast classification of genomes by ANI using skani in GTDB-Tk (by @jfy133 and @prototaxites). ### `Changed` - [#718](https://github.com/nf-core/mag/pull/718) - Refactored all assembly steps into subworkflows (added by @muabnezor) - [#799](https://github.com/nf-core/mag/pull/799) - Add `--cat_classify_unbinned`, to enable taxonomic classification of unbinned contigs using CAT (requested by @amizeranschi, added by @dialvarezs) - [#799](https://github.com/nf-core/mag/pull/799) - Upgraded to latest version of CAT_pack modules (requested by @maxibor, added by @dialvarezs) - [#811](https://github.com/nf-core/mag/pull/811) - Update util modules, and remove aria2 module to replace with native Nextflow downloading of CheckM database (by @dialvarezs) - [#816](https://github.com/nf-core/mag/pull/816) - Removed all leftover references to conda 'defaults' channel (by @jfy133) - [#823](https://github.com/nf-core/mag/pull/823) - Updated to nf-core 3.3.1`TEMPLATE` (by @jfy133 ) - [#827](https://github.com/nf-core/mag/pull/827) - Updated to nf-core 3.3.2`TEMPLATE` (by @dialvarezs) - [#841](https://github.com/nf-core/mag/pull/841) - MultiQC config updated to support CheckM, CheckM2, and GTDB-Tk (by @harper357) - [#844](https://github.com/nf-core/mag/pull/843) - Change loading mechanism of internal PhiX/Lambda databases to improve Dev UX when schema building (by @jfy133) - [#851](https://github.com/nf-core/mag/pull/851) - Improve structure of local modules and subworkflows (by @dialvarezs) - [#853](https://github.com/nf-core/mag/pull/853) - Update nf-core modules and subworkflows (by @dialvarezs) - [#856](https://github.com/nf-core/mag/pull/856) - Update more nf-core modules (by @dialvarezs) ### `Fixed` - [#843](https://github.com/nf-core/mag/pull/843) - Fixed issue with large format Bowtie2 index files not being emitted from index module (reported by Nick Eckersley, fix by @jfy133) - [#847](https://github.com/nf-core/mag/pull/847) - Allow the BBNorm process to use only 0.8 of the memory allocated to the task to stop if from oversubscribing memory (reported by and fix by @erikrikarddaniel) - [#850](https://github.com/nf-core/mag/pull/850) - Fixed some modules of the GDTBTk subworkflow not being represented in version lists (fix by @jfy133) - [#852](https://github.com/nf-core/mag/pull/852) - Fixed version reporting by ensure all modules are represented in final version.yml for MultiQC (by @jfy133) - [#854](https://github.com/nf-core/mag/pull/854) - Update porechop/abi to a patched version to prevent duplicated read names (reported by @palec87, fix by @jfy133) - [#858](https://github.com/nf-core/mag/pull/858) - Fix a single parameter validation failure reporting errors for all parameters by updated nf-schema to 2.5.1 (reported by @Pranjal-Bioinfo, fix by @nvnieuwk and @jfy133) - [#864](https://github.com/nf-core/mag/pull/864) - Fix missing multi-threading of MetaEuk easypredict (reported by @OlivierCoen, fix by @prototaxites). ### `Dependencies` | Tool | Previous version | New version | | ------------ | ---------------- | ----------- | | bcftools | 1.17 | 1.21 | | BUSCO | 5.8.3 | 6.0.0 | | CAT | 5.2.3 | 6.0.1 | | centrifuge | 1.0.4.1 | 1.0.4.2 | | dastool | 1.1.6 | 1.1.7 | | nanolyse | 1.41.6 | 1.44.1 | | fastp | 0.23.4 | 0.24.0 | | flye | | 2.9.5 | | Freebayes | 1.3.6 | 1.3.10 | | geNomad | 1.5.2 | 1.11.0 | | GTDB-Tk | 2.4.0 | 2.5.2 | | metabat2 | 2.15 | 2.17 | | metamdbg | | 1.0 | | minimap2 | | 2.29 | | mmseqs2 | 14.7e284 | 17.b804f | | samtools | | 1.21 | | nf-core | 3.2.0 | 3.3.2 | | pydamage | 0.7.0 | 1.0.0 | | seqtk | 1.3 | 1.4 | | porechop_abi | 0.5.0 | 0.5.0post1 | | NanoPlot | 1.44.1 | 1.46.1 | ### `Deprecated` - [#799](https://github.comf/nf-core/mag/pull/799) - Removed `--cat_official_taxonomy` in favour of `--cat_allow_unofficial_lineages` to control CAT's use of unofficial lineages (added by @dialvarezs) - [#825](https://github.com/nf-core/mag/pull/825) - Removed `--centrifuge_db`, `--kraken2_db`, `--krona_db` and `--skip_krona` parameters following the removal of taxonomic profiling functionality. See nf-core/taxprofiler for replacement (added by @dialvarezs) - [#851](https://github.com/nf-core/mag/pull/851) - Remove `POOL_READ_*` local modules in favor of nf-core cat/fastq (by @dialvarezs) - [#855](https://github.com/nf-core/mag/pull/855) - Remove test_adapterremoval, test_ancient_dna, test_bbnorm, test_busco_auto, test_host_rm, test_hybrid_host_rm, test_binrefinement, test_concoct and test_longread profiles (added by @dialvarezs) - [#864](https://github.com/nf-core/mag/pull/864) - Remove `--gtdb_mash` due to dropping of support by GTDBTk itself (by @prototaxites and @jfy133)

### `Added` - [#730](https://github.com/nf-core/mag/pull/730) - Added `--busco_db_lineage` to allow specifying a specific lineage for BUSCO database (added by @jfy133, @dialvarezs) - [#730](https://github.com/nf-core/mag/pull/730) - Added a new documentation section on database setup (by @jfy133, @dialvarezs) - [#784](https://github.com/nf-core/mag/pull/784) - Added `--bin_min_size` and `--bin_max_size` parameters to filter out bins based on size (requested by @maxibor, @alexhbnr, added by @jfy133, @prototaxites) - [#793](https://github.com/nf-core/mag/pull/793) - Document use of a SquashFS image with `--gtdb_db`, useful for limited inode infrastructure (by @muniheart) - [#805](https://github.com/nf-core/mag/pull/793) - Add support for fastp's `--trim_poly_g` option (by @jfy133) ### `Changed` - [#730](https://github.com/nf-core/mag/pull/730) - Migrate from local BUSCO module to nf-core one, updating version (by @dialvarezs) - [#730](https://github.com/nf-core/mag/pull/730) - Use BUSCO database from nf-core test datasets (by @dialvarezs) - [#788](https://github.com/nf-core/mag/pull/788) - Tweak method of loading GTDB database in GTDBTK_CLASSIFYWF for more stability (reported by @alexhbnr, fix by @jfy133) - [#800](https://github.com/nf-core/mag/pull/800) - Default branch is now set to `main` (by @jfy133 and @mirpedrol) - [#801](https://github.com/nf-core/mag/pull/800) - Increase CheckM memory requests to match [recommended requirements](https://github.com/nf-core/mag/pull/800) (by @jfy133) ### `Fixed` - [#789](https://github.com/nf-core/mag/pull/789) - Improve `--bowtie2_mode` description to clarify default settings (reported by @IceGreb, fix by @jfy133) - [#798](https://github.com/nf-core/mag/pull/798) - Fix overly strict database validation for `--metauk_db` and improve documentation (reported by @ruqse, fix by @jfy133) - [#804](https://github.com/nf-core/mag/pull/804) - Fix broken memory specification for FASTQC (reported by @jmichaelegana, fix by @awgymer & @jfy133) ### `Dependencies` | Tool | Previous version | New version | | -------- | ---------------- | ----------- | | BUSCO | 5.4.3 | 5.8.3 | | csvtk | | 0.31.0 | | nextflow | 24.04.2 | 25.04.2 |

### `Added` - [#745](https://github.com/nf-core/mag/pull/745) - Added pipeline parameter `spades_downstreaminput` to use contigs instead of scaffolds (by @Pranjal-Bioinfo, @jfy133, @GallVp & @sateeshperi). - [#745](https://github.com/nf-core/mag/pull/745) - Added `trimmomatic` as an additional pre-processing tool (by @Pranjal-Bioinfo, @jfy133, @GallVp & @sateeshperi). - [#745](https://github.com/nf-core/mag/pull/745) - Added parameters for `concoct/cut_up_fasta.py` including `bin_concoct_chunksize`, `bin_concoct_overlap` and `bin_concoct_donotconcatlast` (by @Pranjal-Bioinfo, @jfy133, @GallVp & @sateeshperi). - [#777](https://github.com/nf-core/mag/pull/777) - Improved input validation through additional JSON keywords and error messages (by @agusinac) ### `Changed` - [#774](https://github.com/nf-core/mag/pull/774) - Update CheckM2 to v1.1.0 and default database (by @dialvarezs). ### `Fixed` - [#726](https://github.com/nf-core/mag/pull/726) - Fix formatting errors to follow Nextflow best practice (by @dialvarezs). - [#769](https://github.com/nf-core/mag/pull/769) - Fix megahit not emitting correct filenames due to suboptimal arguments ordering (reported and fix by @IceGreb) - [#771](https://github.com/nf-core/mag/pull/771) - Fix misspecified checkm2 database parameter check (reported by @dpelegri and fix by @jfy133) ### `Dependencies` | Tool | Previous version | New version | | ------- | ---------------- | ----------- | | CheckM2 | 1.0.2 | 1.1.0 | | SPAdes | 4.0.0 | 4.1.0 |

### `Added` - [#758](https://github.com/nf-core/mag/pull/758) - Added new diagram in metro-map style (by @jfy133, @prototaxites, @d4straub) ### `Changed` - [#731](https://github.com/nf-core/mag/pull/747) - Updated to nf-core 3.1.2 `TEMPLATE` (by @jfy133) - [#755](https://github.com/nf-core/mag/pull/755) - Updated to nf-core 3.2.0 `TEMPLATE` (by @jfy133) ### `Fixed` - [#748](https://github.com/nf-core/mag/pull/748) - Fix broken phix reference channel when skipping phix removal (reported by @amizeranschi, fix by @muabnezor) - [#752](https://github.com/nf-core/mag/pull/752) - Fix QUAST results not being displayed when skipping certain steps (reported by @amizeranschi, fix by @jfy133) - [#753](https://github.com/nf-core/mag/pull/753) - Fix iGenomes reference support for host removal reference genome (reported by @Thomieh73, fix by @jfy133) - [#759](https://github.com/nf-core/mag/pull/758) - Fixed parameters that allow both files or directories to not error with directories, and general file input validation improvements (reported by @mjfi2sb3, fix by @jfy133)

### `Added` - [#692](https://github.com/nf-core/mag/pull/692) - Added Nanoq as optional longread filtering tool (added by @muabnezor) - [#692](https://github.com/nf-core/mag/pull/692) - Added chopper as optional longread filtering tool and/or phage lambda removal tool (added by @muabnezor) - [#707](https://github.com/nf-core/mag/pull/707) - Make Bin QC a subworkflow (added by @dialvarezs) - [#707](https://github.com/nf-core/mag/pull/707) - Added CheckM2 as an alternative bin completeness and QC tool (added by @dialvarezs) - [#708](https://github.com/nf-core/mag/pull/708) - Added `--exclude_unbins_from_postbinning` parameter to exclude unbinned contigs from post-binning processes, speeding up Prokka in some cases (added by @dialvarezs) - [#732](https://github.com/nf-core/mag/pull/732) - Added support for Prokka's compliance mode with `--prokka_with_compliance --prokka_compliance_centre <xyz>` (reported by @audy and @Thomieh73, added by @jfy133) ### `Changed` - [#731](https://github.com/nf-core/mag/pull/731) - Updated to nf-core 3.1.0 `TEMPLATE` (by @jfy133) ### `Fixed` - [#707](https://github.com/nf-core/mag/pull/708) - Fixed channel passed as GUNC input (added by @dialvarezs) - [#724](https://github.com/nf-core/mag/pull/724) - Fix quoting in `utils_nfcore_mag_pipeline/main.nf` (added by @dialvarezs) - [#716](https://github.com/nf-core/mag/pull/692) - Make short read processing a subworkflow (added by @muabnezor) - [#708](https://github.com/nf-core/mag/pull/708) - Fixed channel passed as GUNC input (added by @dialvarezs) - [#729](https://github.com/nf-core/mag/pull/729) - Fixed misspecified multi-FASTQ input for single-end data in MEGAHIT (reported by John Richards, fix by @jfy133) ### `Dependencies` | Tool | Previous version | New version | | ------- | ---------------- | ----------- | | CheckM | 1.2.1 | 1.2.3 | | CheckM2 | | 1.0.2 | | chopper | | 0.9.0 | | GUNC | 1.0.5 | 1.0.6 | | nanoq | | 0.10.0 |

### `Fixed` - [#707](https://github.com/nf-core/mag/pull/674) - Fix missing space resulting in malformed args for MEGAHIT (reported by @d4straub, fix by @jfy133)

### `Added` - [#674](https://github.com/nf-core/mag/pull/674) - Added `--longread_adaptertrimming_tool` Where user can chose between porechop_abi (default) and porechop (added by @muabnezor) ### `Changed` - [#674](https://github.com/nf-core/mag/pull/674) - Changed to porechop-abi as default adapter trimming tool for long reads. User can still use porechop if preferred (added by @muabnezor) - [#666](https://github.com/nf-core/mag/pull/666) - Update SPAdes to version 4.0.0, replace both METASPADES and MEGAHIT with official nf-core modules (requested by @elsherbini, fix by @jfy133) - [#666](https://github.com/nf-core/mag/pull/666) - Update URLs to GTDB database downloads due to server move (reported by @Jokendo-collab, fix by @jfy133) - [#695](https://github.com/nf-core/mag/pull/695) - Updated to nf-core 3.0.2 `TEMPLATE` (by @jfy133) - [#695](https://github.com/nf-core/mag/pull/695) - Switch more stable Zenodo link for CheckM data (by @jfy133) ### `Fixed` - [#674](https://github.com/nf-core/mag/pull/674) - Make longread preprocessing a subworkflow (added by @muabnezor) - [#674](https://github.com/nf-core/mag/pull/674) - Add porechop and filtlong logs to multiqc (added by @muabnezor) - [#674](https://github.com/nf-core/mag/pull/674) - Change local filtlong module to the official nf-core/filtlong module (added by @muabnezor) - [#690](https://github.com/nf-core/mag/pull/690) - MaxBin2 now using the abundance information from different samples rather than an average (reported by @uel3 and fixed by @d4straub) - [#698](https://github.com/nf-core/mag/pull/698) - Updated prodigal module to not pick up input symlinks for compression causing pigz errors (reported by @zackhenny, fix by @jfy133 ) ### `Dependencies` | Tool | Previous version | New version | | ------------ | ---------------- | ----------- | | Porechop_ABI | | 0.5.0 | | Filtlong | 0.2.0 | 0.2.1 | | SPAdes | 3.15.3 | 4.0.0 |

> [!CAUTION] > This release contains a potentially 'breaking change' for some users. The `--gtdbtk_pplacer_scratch` flag has been replaced with `--gtdbtk_pplacer_useram`. Check the parameter documentation for more details. ### `Added` - [#665](https://github.com/nf-core/mag/pull/648) - Add support for supplying pre-made bowtie host reference index (requested by @simone-pignotti, added by @jfy133) - [#670](https://github.com/nf-core/mag/pull/670) - Added `--gtdbtk_pplacer_useram` to run GTDBTk in memory mode rather than write to disk (requested by @harper357, fixed by @jfy133) ### `Changed` - [#664](https://github.com/nf-core/mag/pull/664) - Update GTDBTk to latest version, with updated column names, update GTDB to release 220 (by @dialvarezs) - [#676](https://github.com/nf-core/mag/pull/676) - Added exit code 12 to valid SPAdes retry codes, due to OOM errors from spades-hammer (reported by @bawee, fix by @jfy133) ### `Fixed` - [#667](https://github.com/nf-core/mag/pull/667) - Fix pipeline crashing if only CONCOCT selected during binning (reported and fixed by @jfy133) - [#670](https://github.com/nf-core/mag/pull/670) - Re-add missing GTDBTk parameters into GTDBTk module (reported by harper357, fixed by @jfy133) - [#672](https://github.com/nf-core/mag/pull/673) - Fix GTDB-Tk per-sample TSV files not being published in output directory (reported by @jhayer, fix by @jfy133) ### `Dependencies` | Tool | Previous version | New version | | ------ | ---------------- | ----------- | | GTDBTk | 2.3.2 | 2.4.0 | ### `Deprecated` - [#670](https://github.com/nf-core/mag/pull/670) - Deprecated `--gtdbtk_pplacer_scratch` due to unintuitive usage (reported by harper357, fixed by @jfy133)