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

• #670 - Deprecated --gtdbtk_pplacer_scratch due to unintuitive usage (reported by harper357, fixed by @jfy133)

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

Changed

• #625 - Updated link to geNomad database for downloading (reported by @amizeranschi, fix by @jfy133)

Fixed

• #618 - Fix CENTRIFUGE mkfifo failures by using work directory /tmp (reported by @skrakau, fix by @jfy133)

Dependencies

Tool	Previous version	New version
Centrifuge	1.0.4_beta	1.0.4.1

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

• #615 - Add new logo (by @jfy133)

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

• #599 - Direct reads input (--input 'sample_{R1,R2}.fastq.gz') is no longer supported, all input must come via samplesheets (by @jfy133)

mag 2.5.4

Changed

• #581 - Added explicit licence text to headers of all custom scripts (reported by @FriederikeHanssen and @maxibor, fix by @jfy133)

Fixed

• #583 - Fix GTDB database input when directory supplied (fix by @jfy133)

mag 2.5.3

Changed

• #575 - Deactivated MetaSPAdes, Centrifuge, and GTDB in test_full profile due to some container incompatibilities in nf-core megatest AWS configurations (by @jfy133)

Fixed

• #574 - Fix wrong channel going to BIN_SUMMARY (fix by @maxibor)

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

• #536 - Remove custom function with native Nextflow for checking file extension (reported by @d4straub, fix by @jfy133)

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).