mag 4.0.0 - Blue Huemul

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

Tool	Previous version	New version
BUSCO	5.4.3	5.8.3
csvtk		0.31.0
nextflow	24.04.2	25.04.2

Deprecated

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

mag 3.4.0 - Green Gecko

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

Tool	Previous version	New version
CheckM2	1.0.2	1.1.0
SPAdes	4.0.0	4.1.0

mag 3.3.1 - [2025-02-13]

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)

mag 3.3.0 - Red Reindeer

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

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

mag 3.2.1 [2024-10-30]

Fixed

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

mag 3.2.0 - Salmon Salmon

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

Tool	Previous version	New version
Porechop_ABI		0.5.0
Filtlong	0.2.0	0.2.1
SPAdes	3.15.3	4.0.0

mag 3.1.0 - Pink Panda

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 - 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)

Changed

• #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)

Fixed

• #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)

Dependencies

Tool	Previous version	New version
GTDBTk	2.3.2	2.4.0

Deprecated

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

3.0.3 [2024-08-27]

Fixed

• #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)

3.0.2 [2024-07-04]

Changed

• #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)

Fixed

• #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)

Dependencies

Tool	Previous version	New version
Porechop	0.2.3_seqan2.1.1	0.2.4
NanoPlot	1.26.3	1.41.6
NanoLyse	1.1.0	1.2.0

mag 3.0.1

Changed

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

Fixed

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

Dependencies

Tool	Previous version	New version
Centrifuge	1.0.4_beta	1.0.4.1