Releases: nf-core/mag
Releases · nf-core/mag
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
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
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
mag 2.5.4
mag 2.5.3
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
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
andmegahit_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 |