Added

• #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)

Changed

• #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)

Fixed

• #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)

Dependencies

Deprecated

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

Added

• #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)

Changed

• #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

Fixed

• #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)

Dependencies

Deprecated

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

Added

• #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)

Changed

• #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)

Fixed

• #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)

Dependencies

Added

• #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).

Changed

• #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)

Fixed

• #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).

Dependencies

Deprecated

• #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)

Added

• #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)

Changed

• #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)

Fixed

• #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)

Dependencies

Deprecated

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

Added

• #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)

Changed

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

Fixed

• #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)

Dependencies

Added

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

Changed

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

Fixed

• #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)

Added

• #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)

Changed

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

Fixed

• #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)

Dependencies

Fixed

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

Added

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

Changed

• #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)

Fixed

• #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 )

Dependencies