Releases: nf-core/mag
Releases · nf-core/mag
mag 3.2.1 [2024-10-30]
mag 3.2.0 - Salmon Salmon
Added
- #674 - Added
--longread_adaptertrimming_toolWhere user can chose between porechop_abi (default) and porechop (added by @muabnezor)
Changed
- #674 - Changed to porechop-abi as default adapter trimming tool for long reads. User can still use porechop if preferred (added by @muabnezor)
- #666 - Update SPAdes to version 4.0.0, replace both METASPADES and MEGAHIT with official nf-core modules (requested by @elsherbini, fix by @jfy133)
- #666 - Update URLs to GTDB database downloads due to server move (reported by @Jokendo-collab, fix by @jfy133)
- #695 - Updated to nf-core 3.0.2
TEMPLATE(by @jfy133) - #695 - Switch more stable Zenodo link for CheckM data (by @jfy133)
Fixed
- #674 - Make longread preprocessing a subworkflow (added by @muabnezor)
- #674 - Add porechop and filtlong logs to multiqc (added by @muabnezor)
- #674 - Change local filtlong module to the official nf-core/filtlong module (added by @muabnezor)
- #690 - MaxBin2 now using the abundance information from different samples rather than an average (reported by @uel3 and fixed by @d4straub)
- #698 - Updated prodigal module to not pick up input symlinks for compression causing pigz errors (reported by @zackhenny, fix by @jfy133 )
Dependencies
| Tool | Previous version | New version |
|---|---|---|
| Porechop_ABI | 0.5.0 | |
| Filtlong | 0.2.0 | 0.2.1 |
| SPAdes | 3.15.3 | 4.0.0 |
Contributors
elsherbini, jfy133, and 5 other contributors
Assets 2
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_useramto 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
Contributors
harper357, bawee, and 4 other contributors
Assets 2
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)
Contributors
harper357, amizeranschi, and 4 other contributors
Assets 2
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 |
Contributors
ChristophKnapp, maxibor, and jfy133
Assets 2
mag 3.0.1
Contributors
skrakau, amizeranschi, and jfy133
Assets 2
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
Contributors
cedwardson4 and jfy133
Assets 2
mag 2.5.4
mag 2.5.3
Contributors
maxibor and jfy133
Assets 2
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)
Contributors
maxibor, jfy133, and 4 other contributors