Releases: nf-core/mag
Releases · nf-core/mag
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
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).