mag: Releases

#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).

#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)

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

See full CHANGELOG for more information

Restructure binning subworkflow in preparation for aDNA workflow and extended binning
Add ancient DNA subworkflow
Add MaxBin2 as second contig binning tool
Add AdapterRemoval2 as an alternative read trimmer
Add DAS Tool for bin refinement
Activate pipeline-specific institutional nf-core/configs
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
Updated some software: fastp 0.20.1 > 0.23.2, MultiQC 1.9 > 1.12
Fix several bugs

See full CHANGELOG for more information