mag 3.0.0 - Magenta Magpie

Caution

This release contains a potentially 'breaking change' for some users. The pipeline no longer directly accepts FASTQ files via --input.
You must use a samplesheet and specify the FASTQs there.

Added

• #615 - Add new logo (by @jfy133)

Changed

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

Fixed

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

Deprecated

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

mag 2.5.4

Changed

• #581 - Added explicit licence text to headers of all custom scripts (reported by @FriederikeHanssen and @maxibor, fix by @jfy133)

Fixed

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

mag 2.5.3

Changed

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

Fixed

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

mag 2.5.2

Added

• #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)

Changed

• #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)

Fixed

• #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)

mag 2.5.1

Fixed

• #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)

Dependencies

Tool	Previous version	New version
CAT	4.6	5.2.3

Deprecated

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

mag 2.5.0 - Aquamarine Kangaroo

Added

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

Changed

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

Fixed

• #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)

Deprecated

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

mag 2.4.0 - Grey Hammerhead

Added

• #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)

Changed

• #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)

Fixed

• #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)

Dependencies

Tool	Previous version	New version
BCFtools	1.16	1.17
SAMtools	1.16.1	1.17
fastp	0.23.2	0.23.4
MultiQC	1.14	1.15

mag 2.3.2

Fixed

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

mag 2.3.1

Fixed

• #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 )

mag 2.3.0 - Red Cow

Added

• #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)

Changed

• #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).

Fixed

• #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)

Dependencies

Tool	Previous version	New version
BUSCO	5.1.0	5.4.3
BCFtools	1.14	1.16
Freebayes	1.3.5	1.3.6
SAMtools	1.15	1.16.1