Releases
2.4.0
mag 2.4.0 - Grey Hammerhead
jfy133
released this
26 Sep 09:01
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
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