The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

• #974 - Re-add accidently removed functionality for using metaSPAdes contigs downstream rather than scaffolds (reported by @Pranjal-Bioinfo, fix by @jfy133)
• #984 - Fix docs regarding usage of Bin QC tool scores when filtering bins for post-processing (by @dialvarezs, @claude)
• #987 - Fix several documentation issues (by @dialvarezs)
• #988 - Fix regarding validation of column long_reads_platform in the input samplesheet (#985 by @vinisalazar)
• #986 - Fix faulty YAML loading (by @jfy133)

• #965 - Add support for the generation of custom contig to bin map files for all bins and refined bins (by @jfy133, @prototaxites)
• #965 - Add support for optional saving of DAS Tool inpout contig2bin map files via --refine_bins_dastool_savecontig2bin, with now singular generation process (by @jfy133, @prototaxites)
• #963 - Add support for outputting and median summarising pyDamage results at bin level when running in ancient DNA mode (by @jfy133)
• #931 - Added ALE (Assembly Likelihood Estimator) for probabilistic assembly quality control (by @PetcuBogdan, @dialvarezs)

• #966 - Replace aria2c downloading of CheckM2 database with native Nextflow downloading due to Zenodo issues (by @jfy133, @dialvarezs)

• #962 - MetaBinner/SemiBin2 are included during bin refinement with DASTool. (by @AlexHoratio)

• #905 - Add nf-test snapshot for test_assembly_input profile (by @dialvarezs)
• #930 - Add binner SemiBin2 (by @d4straub)
• #861 - Added --generate_bigmag_file to execute the bigmag workflow that generates the file to be used as input for BIgMAG (added by @jeffe107)

• #932 - Replaced usages of deprecated Channel() with channel() and fix other LSP warnings (by @dialvarezs)
• #937 - Updated to nf-core 3.5.1 TEMPLATE (by @dialvarezs)
• #938 - Update nf-core modules (by @dialvarezs)

• #894 - Fix read order in metaSPAdes to allow co-assembly of paired-end data of multiple samples (reported by @maartenciers, fix by @jfy133 with contributions from @prototaxites, @d4straub and @dialvarezs)
• #927 - MetaBinner now succeeds when no contigs are too short or all are binned (reported by @MicroSeq, fix by @d4straub)
• #929 - Allow the domain_classification.R script to run with any assembler, not just Megahit or Spades (reported by @MicroSeq, fix by @prototaxites)
• #943 - Fixed concatenation of BUSCO summaries with uneven columns by changing from csvtk to qsv (reported by @jfy133 and @julianu, fix by @dialvarezs)
• #943 - Fixed creation of the Tiara report channel used for concatenation (by @dialvarezs)
• #945 - Skip mixing of GTDB-Tk MultiQC files when binning is skipped (reported by @amizeranschi, fix by @dialvarezs)
• #953 - metaSPAdes retries upon error 250 (out of memory), rather than finishing the pipeline.
• #954 - Skip GTDB-Tk when no bin QC tool is enabled and add warning messages (fix by @dialvarezs)
• #956 - Support long reads assemblers in assembly input (fix by @dialvarezs)

• #943 - Remove csvtk/concat module (by @dialvarezs).

• #842 - Add support for running multiple binQC tools in one run using dedicated --run_busco, --run_checkm, and --run_checkm2 parameters (by @harper357, with contributions from @dialvarezs, @prototaxites and @jfy133)
• #881 - Add binner MetaBinner (by @d4straub, insprired by @HeshamAlmessady & @AlphaSquad)

• #842 - Change bin_summary.tsv format for improved clarity and more comprehensiveness (by @harper357, with contributions from @dialvarezs, @prototaxites and @jfy133)
  • Now will include columns from all bin QC tools executed in a given run (i.e., all/any of BUSCO, CheckM and CheckM2)
  • Adds suffixes to all columns (_<toolname>) to distinguish which column comes from which tool

• #896 - Remove obsolete execution command from README (by @dialvarezs)
• #907 - Include refined bins from all binners in the DASTool/bins output folder (by @AlexHoratio)
• #911 - Ensure column order is consistent when generating depth summaries to prevent swapped results on merged depth summary (by @dialvarezs)
• #912 - Fix validation of multiple sequencing platforms when using binning_map_mode = "all" (reported by @mjfi2sb3, fix by @dialvarezs)
• #921 - Fix publishing of BUSCO files (reported by @joao1980, fix by @dialvarezs)

• #842 - Remove --binqc_tool (by @harper357, with contributions from @dialvarezs, @prototaxites and @jfy133)

• #873 - Document usage of longread_percentidentity and shortread_percentidentity and set the value of longread_percentidentity in the test_full profile to 85 (by @prototaxites)
• #875 - Add binner COMEBin (by @d4straub)

• #878 - Refine test_full config with optimised resource usage for AWS release megatests (by @jfy133)
• #880 - Updated to nf-core 3.4.1 TEMPLATE (by @jfy133)

• #878 - Fix METASPADES process not receiving the correct number of cpus from the fix CPUs parameter (by @jfy133)
• #885 - Fix typo in long-read assembly mode selection (reported by @feixiang1209, fix by @jfy133)
• #888 - Only error if all bins are size filtered if bins have actually been generated (reported by @hkaspersen, fix by @prototaxites)

• #718 - Add support for independent long-read metagenomic assembly (requested by @ljmesi and many others, added by @muabnezor)
• #718 - Added metaMDBG and (meta)Flye as long read assemblers (added by @muabnezor)
• #718 - Added host removal for long reads using minimap2 as aligner (added by @muabnezor)
• #827 - Added nf-test CI testing for all test profiles (added by @jfy133)
• #829 - Add --skip_shortread_qc and --skip_longread_qc params for skipping certain default preprocessing steps (added by @erikrikarddaniel)
• #846 - Improve documentation of group samplesheet column (added by @vinisalazar)
• #855 - Add basic nf-tests for test_longreadonly, test_longreadonly_alternatives, test_hybrid and test_assembly_input (added by @dialvarezs)
• #864 - Add --gtdbtk_skip_aniscreen to disable fast classification of genomes by ANI using skani in GTDB-Tk (by @jfy133 and @prototaxites).

• #718 - Refactored all assembly steps into subworkflows (added by @muabnezor)
• #799 - Add --cat_classify_unbinned, to enable taxonomic classification of unbinned contigs using CAT (requested by @amizeranschi, added by @dialvarezs)
• #799 - Upgraded to latest version of CAT_pack modules (requested by @maxibor, added by @dialvarezs)
• #811 - Update util modules, and remove aria2 module to replace with native Nextflow downloading of CheckM database (by @dialvarezs)
• #816 - Removed all leftover references to conda 'defaults' channel (by @jfy133)
• #823 - Updated to nf-core 3.3.1TEMPLATE (by @jfy133 )
• #827 - Updated to nf-core 3.3.2TEMPLATE (by @dialvarezs)
• #841 - MultiQC config updated to support CheckM, CheckM2, and GTDB-Tk (by @harper357)
• #844 - Change loading mechanism of internal PhiX/Lambda databases to improve Dev UX when schema building (by @jfy133)
• #851 - Improve structure of local modules and subworkflows (by @dialvarezs)
• #853 - Update nf-core modules and subworkflows (by @dialvarezs)
• #856 - Update more nf-core modules (by @dialvarezs)

• #843 - Fixed issue with large format Bowtie2 index files not being emitted from index module (reported by Nick Eckersley, fix by @jfy133)
• #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 - Fixed some modules of the GDTBTk subworkflow not being represented in version lists (fix by @jfy133)
• #852 - Fixed version reporting by ensure all modules are represented in final version.yml for MultiQC (by @jfy133)
• #854 - Update porechop/abi to a patched version to prevent duplicated read names (reported by @palec87, fix by @jfy133)
• #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 - Fix missing multi-threading of MetaEuk easypredict (reported by @OlivierCoen, fix by @prototaxites).

• #799 - Removed --cat_official_taxonomy in favour of --cat_allow_unofficial_lineages to control CAT's use of unofficial lineages (added by @dialvarezs)
• #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 - Remove POOL_READ_* local modules in favor of nf-core cat/fastq (by @dialvarezs)
• #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 - Remove --gtdb_mash due to dropping of support by GTDBTk itself (by @prototaxites and @jfy133)

• #730 - Added --busco_db_lineage to allow specifying a specific lineage for BUSCO database (added by @jfy133, @dialvarezs)
• #730 - Added a new documentation section on database setup (by @jfy133, @dialvarezs)
• #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 - Document use of a SquashFS image with --gtdb_db, useful for limited inode infrastructure (by @muniheart)
• #805 - Add support for fastp's --trim_poly_g option (by @jfy133)

• #730 - Migrate from local BUSCO module to nf-core one, updating version (by @dialvarezs)
• #730 - Use BUSCO database from nf-core test datasets (by @dialvarezs)
• #788 - Tweak method of loading GTDB database in GTDBTK_CLASSIFYWF for more stability (reported by @alexhbnr, fix by @jfy133)
• #800 - Default branch is now set to main (by @jfy133 and @mirpedrol)
• #801 - Increase CheckM memory requests to match recommended requirements (by @jfy133)

• #789 - Improve --bowtie2_mode description to clarify default settings (reported by @IceGreb, fix by @jfy133)
• #798 - Fix overly strict database validation for --metauk_db and improve documentation (reported by @ruqse, fix by @jfy133)
• #804 - Fix broken memory specification for FASTQC (reported by @jmichaelegana, fix by @awgymer & @jfy133)

• #730 - Remove --busco_auto_lineage_prok due to update and simplified usage of BUSCO (added by @jfy133, @dialvarezs)

• #745 - Added pipeline parameter spades_downstreaminput to use contigs instead of scaffolds (by @Pranjal-Bioinfo, @jfy133, @GallVp & @sateeshperi).
• #745 - Added trimmomatic as an additional pre-processing tool (by @Pranjal-Bioinfo, @jfy133, @GallVp & @sateeshperi).
• #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 - Improved input validation through additional JSON keywords and error messages (by @agusinac)
• #784 - Add ability to filter out bins based on bin size for downstream using --bin_min_size, --bin_max_size (reported by @maxibor & @alexhbnr, fix by @jfy133)

• #774 - Update CheckM2 to v1.1.0 and default database (by @dialvarezs).

• #726 - Fix formatting errors to follow Nextflow best practice (by @dialvarezs).
• #769 - Fix megahit not emitting correct filenames due to suboptimal arguments ordering (reported and fix by @IceGreb)
• #771 - Fix misspecified checkm2 database parameter check (reported by @dpelegri and fix by @jfy133)

• #758 - Added new diagram in metro-map style (by @jfy133, @prototaxites, @d4straub)

• #731 - Updated to nf-core 3.1.2 TEMPLATE (by @jfy133)
• #755 - Updated to nf-core 3.2.0 TEMPLATE (by @jfy133)

• #748 - Fix broken phix reference channel when skipping phix removal (reported by @amizeranschi, fix by @muabnezor)
• #752 - Fix QUAST results not being displayed when skipping certain steps (reported by @amizeranschi, fix by @jfy133)
• #753 - Fix iGenomes reference support for host removal reference genome (reported by @Thomieh73, fix by @jfy133)
• #759 - 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)

• #692 - Added Nanoq as optional longread filtering tool (added by @muabnezor)
• #692 - Added chopper as optional longread filtering tool and/or phage lambda removal tool (added by @muabnezor)
• #707 - Make Bin QC a subworkflow (added by @dialvarezs)
• #707 - Added CheckM2 as an alternative bin completeness and QC tool (added by @dialvarezs)
• #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 - Added support for Prokka's compliance mode with --prokka_with_compliance --prokka_compliance_centre <xyz> (reported by @audy and @Thomieh73, added by @jfy133)

• #731 - Updated to nf-core 3.1.0 TEMPLATE (by @jfy133)

• #707 - Fixed channel passed as GUNC input (added by @dialvarezs)
• #724 - Fix quoting in utils_nfcore_mag_pipeline/main.nf (added by @dialvarezs)
• #716 - Make short read processing a subworkflow (added by @muabnezor)
• #708 - Fixed channel passed as GUNC input (added by @dialvarezs)
• #729 - Fixed misspecified multi-FASTQ input for single-end data in MEGAHIT (reported by John Richards, fix by @jfy133)

• #707 - Fix missing space resulting in malformed args for MEGAHIT (reported by @d4straub, fix by @jfy133)

• #674 - Added --longread_adaptertrimming_tool Where user can chose between porechop_abi (default) and porechop (added by @muabnezor)

• #674 - Changed to porechop-abi as default adapter trimming tool for long reads. User can still use porechop if preferred (added by @muabnezor)
• #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 - Update URLs to GTDB database downloads due to server move (reported by @Jokendo-collab, fix by @jfy133)
• #695 - Updated to nf-core 3.0.2 TEMPLATE (by @jfy133)
• #695 - Switch more stable Zenodo link for CheckM data (by @jfy133)

• #674 - Make longread preprocessing a subworkflow (added by @muabnezor)
• #674 - Add porechop and filtlong logs to multiqc (added by @muabnezor)
• #674 - Change local filtlong module to the official nf-core/filtlong module (added by @muabnezor)
• #690 - MaxBin2 now using the abundance information from different samples rather than an average (reported by @uel3 and fixed by @d4straub)
• #698 - Updated prodigal module to not pick up input symlinks for compression causing pigz errors (reported by @zackhenny, fix by @jfy133 )

• #665 - Add support for supplying pre-made bowtie host reference index (requested by @simone-pignotti, added by @jfy133)
• #670 - Added --gtdbtk_pplacer_useram to run GTDBTk in memory mode rather than write to disk (requested by @harper357, fixed by @jfy133)

• #664 - Update GTDBTk to latest version, with updated column names, update GTDB to release 220 (by @dialvarezs)
• #676 - Added exit code 12 to valid SPAdes retry codes, due to OOM errors from spades-hammer (reported by @bawee, fix by @jfy133)

• #667 - Fix pipeline crashing if only CONCOCT selected during binning (reported and fixed by @jfy133)
• #670 - Re-add missing GTDBTk parameters into GTDBTk module (reported by harper357, fixed by @jfy133)
• #672 - Fix GTDB-Tk per-sample TSV files not being published in output directory (reported by @jhayer, fix by @jfy133)

• #670 - Deprecated --gtdbtk_pplacer_scratch due to unintuitive usage (reported by harper357, fixed by @jfy133)

• #648 - Fix sample ID/assembly ID check failure when no IDs match (reported by @zackhenny, fix by @prototaxites)
• #646 - GTDB-Tk directory input now creates a value channel so it runs for all entries to the process and not just the first (reported by @amizeranschi, fix by @prototaxites).
• #639 - Fix pipeline failure when a sample produces only a single bin (fix by @d-callan)
• #651 - Replace base container for bash only modules to reduce number of containers in pipeline (reported and fixed by @harper357)
• #652 - Fix documentation typo in using user-defined assembly parameters (reported and fixed by @amizeranschi)
• #653 - Fix overwriting of per-bin 'raw' GUNC RUN output files (multi-bin summary tables not affected) (reported by @zackhenny and fixed by @jfy133)

• #633 - Changed BUSCO to use offline mode when the database is specified by the user (reported by @ChristophKnapp and many others, fix by @jfy133)
• #632 - Use default NanoLyse log of just removed reads rather than custom (by @jfy133)

• #630 - Fix CONCOCT empty bins killing the pipeline, and allow for true multithreading again (removing OPENBLAS loop) (reported by @maxibor, fix by @maxibor and @jfy133)

• #625 - Updated link to geNomad database for downloading (reported by @amizeranschi, fix by @jfy133)

• #618 - Fix CENTRIFUGE mkfifo failures by using work directory /tmp (reported by @skrakau, fix by @jfy133)

• #615 - Add new logo (by @jfy133)

• #599 - Update to nf-core v2.13.1 TEMPLATE (by @jfy133)
• #614 - Update to nf-core v2.14.1 TEMPLATE (by @jfy133)

• #606 - Prevent pipeline crash when premade mashdb given to or no alignments found with GTDB-TK_CLASSIFYWF (reported by @cedwardson4, fix by @jfy133)

• #599 - Direct reads input (--input 'sample_{R1,R2}.fastq.gz') is no longer supported, all input must come via samplesheets (by @jfy133)

• #581 - Added explicit licence text to headers of all custom scripts (reported by @FriederikeHanssen and @maxibor, fix by @jfy133)
• #602 - Co-binning when using aDNA mode now enabled (added by @maxibor)

• #583 - Fix GTDB database input when directory supplied (fix by @jfy133)

• #575 - Deactivated MetaSPAdes, Centrifuge, and GTDB in test_full profile due to some container incompatibilities in nf-core megatest AWS configurations (by @jfy133)

• #574 - Fix wrong channel going to BIN_SUMMARY (fix by @maxibor)

• #562 - Add CAT summary into the global bin_summary (by @maxibor)
• #565 - Add warning of empty GTDB-TK results if no contigs pass completeness filter (by @jfy133 and @maxibor)

• #563 - Update to nf-core v2.12 TEMPLATE (by @CarsonJM)
• #566 - More logical ordering of MultiQC sections (assembly and bin sections go together respectively) (fix by @jfy133)

• #548 - Fixes to (reported by @maxibor, @PPpissar, @muniheart, @llborcard, fix by @maxibor)
  • GTDBK-TK execution
  • CAT/QUAST/DEPTH bin summary file name collisions
  • BUSCO database parsing
  • Correct CAT name files
• #558 - Fix bug in run merging when dealing with single end data (reported by @roberta-davidson, fix by @jfy133)

• #489 - Fix file name collision clashes for CHECKM, CAT, GTDBTK, and QUAST (reported by @tillenglert and @maxibor, fix by @maxibor)
• #533 - Fix glob pattern for publishing MetaBAT2 bins in results (reported by @patriciatran, fix by @jfy133)
• #535 - Fix input validation pattern to again allow direct FASTQ input (reported by @lennijusten, @emnilsson, fix by @jfy133, @d4straub, @mahesh-panchal, @nvnieuwk)

• #536 - Remove custom function with native Nextflow for checking file extension (reported by @d4straub, fix by @jfy133)

• #504 - New parameters --busco_db, --kraken2_db, and --centrifuge_db now support directory input of a pre-uncompressed database archive directory (by @gregorysprenger).

• #511 - Update to nf-core 2.10 TEMPLATE (by @jfy133)
• #504 - --save_busco_reference is now replaced by --save_busco_db (by @gregorysprenger).

• #514 - Fix missing CONCOCT files in downstream output (reported by @maxibor, fix by @jfy133)
• #515 - Fix overwriting of GUNC output directories when running with domain classification (reported by @maxibor, fix by @jfy133)
• #516 - Fix edge-case bug where MEGAHIT re-uses previous work directory on resume and fails (reported by @husensofteng, fix by @prototaxites)
• #520 - Fix missing Tiara output files (fix by @jfy133)
• #522 - Fix 'nulls' in depth plot PNG files (fix by @jfy133)

• #504 - --busco_reference, --busco_download_path, --save_busco_reference parameters have been deprecated and replaced with new parameters (by @gregorysprenger).

• #497 - Adds support for pointing at a local db for krona, using the parameter --krona_db (by @willros).
• #395 - Adds support for fast domain-level classification of bins using Tiara, to allow bins to be separated into eukaryotic and prokaryotic-specific processes.
• #422 - Adds support for normalization of read depth with BBNorm (added by @erikrikarddaniel and @fabianegli)
• #439 - Adds ability to enter the pipeline at the binning stage by providing a CSV of pre-computed assemblies (by @prototaxites)
• #459 - Adds ability to skip damage correction step in the ancient DNA workflow and just run pyDamage (by @jfy133)
• #364 - Adds geNomad nf-core modules for identifying viruses in assemblies (by @PhilPalmer and @CarsonJM)
• #481 - Adds MetaEuk for annotation of eukaryotic MAGs, and MMSeqs2 to enable downloading databases for MetaEuk (by @prototaxites)
• #437 - --gtdb_db also now supports directory input of an pre-uncompressed GTDB archive directory (reported by @alneberg, fix by @jfy133)
• #494 - Adds support for saving the BAM files from Bowtie2 mapping of input reads back to assembly (fix by @jfy133)

• #428 #467 - Update to nf-core 2.8, 2.9 TEMPLATE (by @jfy133)
• #429 - Replaced hardcoded CheckM database auto-download URL to a parameter (reported by @erikrikarddaniel, fix by @jfy133)
• #441 - Deactivated CONCOCT in AWS 'full test' due to very long runtime (fix by @jfy133).
• #442 - Remove warning when BUSCO finds no genes in bins, as this can be expected in some datasets (reported by @Lumimar, fix by @jfy133).
• #444 - Moved BUSCO bash code to script (by @jfy133)
• #477 - --gtdb parameter is split into --skip_gtdbtk and --gtdb_db to allow finer control over GTDB database retrieval (fix by @jfy133)
• #500 - Temporarily disabled downstream processing of both refined and raw bins due to bug (by @jfy133)

• #496 - Fix help text for paramters --bowtie2_mode, spades_options and megahit_options (by @willros)
• #400 - Fix duplicated Zenodo badge in README (by @jfy133)
• #406 - Fix CheckM database always downloading, regardless if CheckM is selected (by @jfy133)
• #419 - Fix bug with busco_clean parameter, where it is always activated (by @prototaxites)
• #426 - Fixed typo in help text for parameters --host_genome and --host_fasta (by @tillenglert)
• #434 - Fix location of samplesheet for AWS full tests (reported by @Lfulcrum, fix by @jfy133)
• #438 - Fixed version inconsistency between conda and containers for GTDBTK_CLASSIFYWF (by @jfy133)
• #439 - Fix bug in assembly input (by @prototaxites)
• #447 - Remove default: None from parameter schema (by @drpatelh)
• #449 - Fix results file overwriting in Ancient DNA workflow (reported by @alexhbnr, fix by @jfy133)
• #470 - Fix binning preparation from running even when binning was requested to be skipped (reported by @prototaxites, fix by @jfy133)
• #480 - Improved -resume reliability through better meta map preservation (reported by @prototaxites, fix by @jfy133)
• #493 - Update METABAT2 nf-core module so that it reduced the number of unnecessary file moves, enabling virtual filesystems (fix by @adamrtalbot)
• #500 - Fix MaxBin2 bins not being saved in results directly properly (reported by @Perugolate, fix by @jfy133)

• #461 - Fix full-size AWS test profile paths (by @jfy133)
• #461 - Fix pyDamage results being overwritten (reported by @alexhbnr, fix by @jfy133)

• #458 - Correct the major issue in ancient DNA workflow of binning refinement being performed on uncorrected contigs instead of aDNA consensus recalled contigs (issue #449)
• #451 - Fix results file overwriting in Ancient DNA workflow (reported by @alexhbnr, fix by @jfy133, and integrated by @maxibor in #458 )

• #350 - Adds support for CheckM as alternative bin completeness and QC tool (added by @jfy133 and @skrakau)
• #353 - Added the busco_clean parameter to optionally clean each BUSCO directory after a successful (by @prototaxites)
• #361 - Added the skip_clipping parameter to skip read preprocessing with fastp or adapterremoval. Running the pipeline with skip_clipping, keep_phix and without specifying a host genome or fasta file skips the FASTQC_TRIMMED process (by @prototaxites)
• #365 - Added CONCOCT as an additional (optional) binning tool (by @jfy133)
• #366 - Added CAT_SUMMARISE process and cat_official_taxonomy parameter (by @prototaxites)
• #372 - Allow CAT_DB to take an extracted database as well as a tar.gz file (by @prototaxites).
• #380 - Added support for saving processed reads (clipped, host removed etc.) to results directory (by @jfy133)
• #394 - Added GUNC for additional chimeric bin/contamination QC (added by @jfy133)

• #340,#368,#373 - Update to nf-core 2.7.2 TEMPLATE (by @jfy133, @d4straub, @skrakau)
• #373 - Removed parameter --enable_conda. Updated local modules to new conda syntax and updated nf-core modules (by @skrakau)
• #385 - CAT also now runs on unbinned contigs as well as binned contigs (added by @jfy133)
• #399 - Removed undocumented BUSCO_PLOT process (previously generated *.busco_figure.png plots unsuitable for metagenomics) (by @skrakau).
• #416 - Use GTDBTK_CLASSIFYWF nf-core module instead of local module (added by @alxndrdiaz)

• #345 - Bowtie2 mode changed to global alignment for ancient DNA mode (--very-sensitive mode) to prevent soft clipping at the end of reads when running in local mode. (by @maxibor)
• #349 - Add a warning that pipeline will reset minimum contig size to 1500 specifically MetaBAT2 process, if a user supplies below this threshold. (by @jfy133)
• #352 - Escape the case in the BUSCO module that BUSCO can just detect a root lineage but is not able to find any marker genes (by @alexhbnr)
• #355 - Include error code 21 for retrying with higher memory for SPAdes and hybridSPAdes (by @mglubber)

• #328 - Fix too many symbolic links issue in local convert_depths module (reported by @ChristophKnapp and fixed by @apeltzer, @jfy133)
• #329 - Each sample now gets it's own result directory for PyDamage analysis and filter (reported and fixed by @maxibor)

• #263 - Restructure binning subworkflow in preparation for aDNA workflow and extended binning
• #247 - Add ancient DNA subworkflow
• #263 - Add MaxBin2 as second contig binning tool
• #285 - Add AdapterRemoval2 as an alternative read trimmer
• #291 - Add DAS Tool for bin refinement
• #319 - Activate pipeline-specific institutional nf-core/configs

• #269,#283,#289,#302 - Update to nf-core 2.4 TEMPLATE
• #286 - Cite our publication instead of the preprint
• #291, #299 - Add extra results folder GenomeBinning/depths/contigs for [assembler]-[sample/group]-depth.txt.gz, and GenomeBinning/depths/bins for bin_depths_summary.tsv and [assembler]-[binner]-[sample/group]-binDepths.heatmap.png
• #315 - Replace base container for standard shell tools to fix problems with running on Google Cloud

• #290 - Fix caching of binning input
• #305 - Add missing Bowtie2 version for process BOWTIE2_PHIX_REMOVAL_ALIGN to software_versions.yml
• #307 - Fix retrieval of GTDB-Tk version (note about newer version caused error in CUSTOM_DUMPSOFTWAREVERSIONS)
• #309 - Fix publishing of BUSCO busco_downloads/ folder, i.e. publish only when --save_busco_reference is specified
• #321 - Fix parameter processing in BOWTIE2_REMOVAL_ALIGN (which was erroneously for BOWTIE2_PHIX_REMOVAL_ALIGN)

• #240 - Add prodigal to predict protein-coding genes for assemblies.
• #241 - Add parameter --skip_prodigal.
• #244 - Add pipeline preprint information.
• #245 - Add Prokka to annotate binned genomes.

• #249 - Update workflow overview figure.
• #258 - Updated MultiQC 1.9 to 1.11.
• #260 - Updated SPAdes 3.13.1 -> 3.15.3, MEGAHIT 1.2.7 -> 1.2.7

• #256 - Fix --skip_busco.
• #236 - Fix large assemblies (> 4 billion nucleotides in length).
• #254 - Fix MetaBAT2 error with nextflow version 21.10.x (21.04.03 is the latest functional version for nf-core/mag 2.1.0).
• #255 - Update gtdbtk conda channel.
• #258 - FastP results are now in MultiQC.

• #212, #214 - Add bin abundance estimation based on median sequencing depths of corresponding contigs (results are written to results/GenomeBinning/bin_depths_summary.tsv and results/GenomeBinning/bin_summary.tsv) #197.
• #214 - Add generation of (clustered) heat maps with bin abundances across samples (using centered log-ratios)
• #217 - Publish genes predicted with Prodigal within BUSCO run (written to results/GenomeBinning/QC/BUSCO/[assembler]-[bin]_prodigal.gff).

• #218 - Update to nf-core 2.0.1 TEMPLATE (DSL2)

• #226 - Fix handling of BUSCO output when run in auto lineage selection mode and selected specific lineage is the same as the generic one.

• #179 - Add BUSCO automated lineage selection functionality (new default). The pameter --busco_auto_lineage_prok can be used to only consider prokaryotes and the parameter --busco_download_path to run BUSCO in offline mode.
• #178 - Add taxonomic bin classification with GTDB-Tk v1.5.0 (for bins filtered based on BUSCO QC metrics).
• #196 - Add process for CAT database creation as an alternative to using pre-built databases.

• #162 - Switch to DSL2
• #162 - Changed --input file format from TSV to CSV format, requires header now
• #162 - Update README.md, docs/usage.md and docs/output.md
• #162 - Update FastP from version 0.20.0 to 0.20.1
• #162 - Update Bowtie2 from version 2.3.5 to 2.4.2
• #162 - Update FastQC from version 0.11.8 to 0.11.9
• #172 - Compressed discarded MetaBAT2 output files
• #176 - Update CAT DB link
• #179 - Update BUSCO from version 4.1.4 to 5.1.0
• #179 - By default BUSCO now performs automated lineage selection instead of using the bacteria_odb10 lineage as reference. Specific lineage datasets can still be provided via --busco_reference.
• #178 - Change output file: results/GenomeBinning/QC/quast_and_busco_summary.tsv -> results/GenomeBinning/bin_summary.tsv, contains GTDB-Tk results as well.
• #191 - Update to nf-core 1.14 TEMPLATE
• #193 - Compress CAT output files #180
• #198 - Requires nextflow version >= 21.04.0
• #200 - Small changes in GitHub Actions tests
• #203 - Renamed fastp params and improved description in documentation: --mean_quality -> --fastp_qualified_quality, --trimming_quality -> --fastp_cut_mean_quality

• #175 - Fix bug in retrieving the --max_unbinned_contigs longest unbinned sequences that are longer than --min_length_unbinned_contigs (split_fasta.py)
• #175 - Improved runtime of split_fasta.py in METABAT2 process (important for large assemblies, e.g. when computing co-assemblies)
• #194 - Allow different folder structures for Kraken2 databases containing *.k2d files #187
• #195 - Fix documentation regarding required compression of input FastQ files #160
• #196 - Add process for CAT database creation as solution for problem caused by incompatible DIAMOND version used for pre-built CAT database and CAT classification #90, #188

• #146 - Add --coassemble_group parameter to allow group-wise co-assembly
• #146 - Add --binning_map_mode parameter allowing different mapping strategies to compute co-abundances used for binning (all, group, own)
• #149 - Add two new parameters to allow custom SPAdes and MEGAHIT options (--spades_options and --megahit_options)

• #141 - Update to nf-core 1.12.1 TEMPLATE
• #143 - Manifest file has to be handed over via --input parameter now
• #143 - Changed format of manifest input file: requires a '.tsv' suffix and additionally contains group ID
• #143 - TSV --input file allows now also entries containing only short reads
• #145 - When using TSV input files, uses sample IDs now for FastQC instead of basenames of original read files. Allows non-unique file basenames.

• #143 - Change parameter: --manifest -> --input

• #135 - Update to nf-core 1.12 TEMPLATE

• #133 - Fixed processing of --input parameter #131

• #121 - Add full-size test
• #124 - Add worfklow overview figure to README

• #123 - Update to new nf-core 1.11 TEMPLATE

• #118 - Fix seaborn to v0.10.1 to avoid nanoplot error
• #120 - Fix link to CAT database in help message
• #124 - Fix description of CAT process in output.md

• #35 - Add social preview image
• #49 - Add host read removal with Bowtie 2 and according custom section to MultiQC
• #49 - Add separate MultiQC section for FastQC after preprocessing
• #65 - Add MetaBAT2 RNG seed parameter --metabat_rng_seed and set the default to 1 which ensures reproducible binning results
• #65 - Add parameters --megahit_fix_cpu_1, --spades_fix_cpus and --spadeshybrid_fix_cpus to ensure reproducible results from assembly tools
• #66 - Export depth.txt.gz into result folder
• #67 - Compress assembly files
• #82 - Add nextflow_schema.json
• #104 - Add parameter --save_busco_reference

• #56 - Update MetaBAT2 from v2.13 to v2.15
• #46 - Update MultiQC from v1.7 to v1.9
• #88 - Update to new nf-core 1.10.2 TEMPLATE
• #88 - --reads is now removed, use --input instead
• #101 - Prevented PhiX alignments from being stored in work directory #97
• #104, #111 - Update BUSCO from v3.0.2 to v4.1.4

• #29 - Fix MetaBAT2 binning discards unbinned contigs #27
• #31, #36, #76, #107 - Fix links in README
• #47 - Fix missing MultiQC when --skip_quast or --skip_busco was specified
• #49, #89 - Added missing parameters to summary
• #50 - Fix missing channels when --keep_phix is specified
• #54 - Updated links to minikraken db
• #54 - Fixed Kraken2 dp preparation: allow different names for compressed archive file and contained folder as for some minikraken dbs
• #55 - Fixed channel joining for multiple samples causing MetaBAT2 error #32
• #57 - Fix number of threads used by MetaBAT2 program jgi_summarize_bam_contig_depths
• #70 - Fix SPAdes memory conversion issue #61
• #71 - No more ignoring errors in SPAdes assembly
• #72 - No more ignoring of BUSCO errors
• #73, #75 - Improved output documentation
• #96 - Fix missing bin names in MultiQC BUSCO section #78
• #104 - Fix BUSCO errors causing missing summary output #77

• #29 - Change depreciated parameters: --singleEnd -> --single_end, --igenomesIgnore -> --igenomes_ignore

Initial release of nf-core/mag, created with the nf-core template.

• short and long reads QC (fastp, porechop, filtlong, fastqc)
• Lambda and PhiX detection and filtering (bowtie2, nanolyse)
• Taxonomic classification of reads (centrifuge, kraken2)
• Short read and hybrid assembly (megahit, metaspades)
• metagenome binning (metabat2)
• QC of bins (busco, quast)
• annotation (cat/bat)