Releases: nf-core/taxprofiler
Releases · nf-core/taxprofiler
v1.2.1 - Bouncy Basenji Patch [2024-11-28]
Added
Fixed
- #550 Fixed a bug where single-end data with the same sample names that include
.
in it would overwrite output files (❤️ to @SannaAb for reporting, fixed by @Midnighter)
- #552 Fixed the issue where nonpareil fails due to insufficient data for calculation caused by a missing PNG (❤️ to @Joon-Klaps for reporting, fixed by @LilyAnderssonLee)
Dependencies
Deprecated
v1.2.0 - Bouncy Basenji [2024-10-03]
Added
Fixed
- #518 Fixed a bug where Oxford Nanopore FASTA input files would not be processed (❤️ to @ikarls for reporting, fixed by @jfy133)
- #523 Removed hardcoded
-m lca
from GANON_CLASSIFY due to more options in new version of ganon (fixed by @LilyAnderssonLee & @jfy133)
- #531 Fix FASTA input validation in schema allowing FASTQ extension, expand allowed FASTA extensions (fixed by @jfy133)
- #512 Minor formatting and ordering improvements in MultiQC report (by @jfy133)
- #532 - Added missing documentation behind the 'ignore' BRACKEN_BRACKEN error strategy (❤️ to @Mavti for reporting, fixed by @jfy133)
- #536 - Redefine
contents_re
for filtlong to fix its missing from the MultiQC report (fixed by @LilyAnderssonLee)
Dependencies
Tool |
Previous version |
New version |
bbmap |
39.01 |
39.06 |
bowtie2 |
2.4.4 |
2.5.2 |
bracken |
2.7 |
2.9 |
diamond |
2.0.15 |
2.1.8 |
ganon |
1.5.1 |
2.0.0 |
kraken2 |
2.1.2 |
2.1.3 |
krona |
2.8 |
2.8.1 |
megan |
6.24.20 |
6.25.9 |
metaphlan |
4.0.6 |
4.1.1 |
minimap2 |
2.24 |
2.28 |
motus |
3.0.3 |
3.1.0 |
multiqc |
1.21 |
1.25 |
samtools |
1.17 |
1.20 |
Deprecated
v1.1.8 - Augmented Akita Patch [2024-06-20]
Added
- #487 Updated to nf-core pipeline template v2.14.1 (added by @jfy133)
Fixed
- #484 Improved input validation to immediately fail if run accession IDs within a given sample ID are not unique (❤️ to @sofstam for reporting, fixed by @jfy133)
- #491 Added flag to publish intermediate bracken files (❤️ to @ewissel for reporting, fixed by @sofstam and @jfy133)
- #489 Fix KrakenUniq classified reads output format mismatch (❤️ to @SannaAb for reporting, fixed by @jfy133)
- #495 Stop TAXPASTA failures when profiles do not have exact compositionality (fixes by @Midnighter, @jfy133)
Dependencies
Tool |
Previous version |
New version |
KMCP |
0.9.1 |
0.9.4 |
TAXPASTA |
0.6.1 |
0.7.0 |
Deprecated
- #492 Removed
--kmcp_mode
parameter from KMCP to allow per database specification by setting in db_params in database sheet (fixed by @jfy133)
v1.1.7 - Augmented Akita Patch [2024-04-29]
Added
- #477 Provide more emphasis and links to tutorials on how to retrieve and supply reference databases (❤️ to @vmkalbskopf for reporting, added by @jfy133)
Fixed
Dependencies
Deprecated
v1.1.6 - Augmented Akita Patch [2024-04-16]
Added
- #454 Updated to nf-core pipeline template v2.13.1 (added by @LilyAnderssonLee & @sofstam)
- #461 Turned on 'strict' Nextflow evaluation runs (added by @jfy133)
- #461 Optimised database compression so each compressed input database is untarred once, and shared amongst each run with different parameters (added by @jfy133)
- #461 Added new parameter to optionally save uncompressed databases (added by @jfy133)
- #471 Removed
-stub
run in the download_pipeline.yml
because the pipeline does not support stub runs on dev (fixed by @LilyAnderssonLee)
Fixed
- #336 Replaced samplesheet check with nf-validation for both sample and database input sheets (fix by @LilyAnderssonLee)
- #460 Corrected the channel transformations to combine Kaiju and mOTUs reports with their reference databases (fix by @Midnighter)
v1.1.5 - Augmented Akita Patch [2024-02-08]
Added
- #439 Read deduplication with fastp (added by @maxibor)
- #440 Include mention of pre-built kaiju databases in tutorial.md (added by @Joon-Klaps)
- #442 Updated to nf-core pipeline template v2.12 (added by @sofstam)
Fixed
- #444 Centrifuge now uses dedicated tmp directory to hopefully prevent mkfifo clashes (❤️ to @erinyoung for reporting, fix by @jfy133)
Dependencies
Tool |
Previous version |
New version |
Centrifuge |
1.0.4_beta |
1.0.4.1 |
v1.1.4 - Augmented Akita Patch [2024-01-24]
Fixed
Dependencies
Tool |
Previous version |
New version |
kaiju |
1.8.2 |
1.10.0 |
v1.1.3 - Augmented Akita Patch [2024-01-12]
Added
Fixed
- #419 Added improved syntax highlighting for tables in documentation (fix by @mashehu)
- #421 Updated the krakenuniq/preloadedkrakenuniq module that contained a fix for saving the output reads (❤️ to @SannaAb for reporting, fix by @Midnighter)
- #427 Fixed preprint information in the recommended methods text (fix by @jfy133)
Dependencies
Tool |
Previous version |
New version |
multiqc |
1.15 |
1.19 |
fastqc |
11.9 |
12.1 |
nf-validation |
unpinned |
1.1.3 |
v1.1.2 - Augmented Akita Patch [2023-10-27]
Added
- #408 Added preprint citation information to README and manifest (added by @jfy133)
Fixed
- #405 Fix database to tool mismatching in KAIJU2KRONA input (❤️ to @MajoroMask for reporting, fix by @jfy133)
- #406 Fix overwriting of bracken-derived kraken2 outputs when the database name is shared between Bracken/Kraken2. (❤️ to @MajoroMask for reporting, fix by @jfy133)
- #409 Fix a NullPointerException error occurring occasionally in older version of MEGAN's rma2info (❤️ to @MajoroMask for reporting, fix by @jfy133)
Dependencies
Tool |
Previous version |
New version |
megan/rma2info |
6.21.7 |
6.24.20 |
v1.1.1 - Augmented Akita Patch [2023-10-11]
Added
Fixed
- #383 Update the module of KrakenUniq to the latest to account for edge case bugs where FASTQ input was mis-detected as wrong format (❤️ to @asafpr for reporting and solution, fixed by @LilyAnderssonLee)
- #392 Update the module of Taxpasta to support adding taxa information to results (❤️ to @SannaAb for reporting, fixed by @Midnighter)
Dependencies
Tool |
Previous version |
New version |
KrakenUniq |
1.0.2 |
1.0.4 |
taxpasta |
0.6.0 |
0.6.1 |
Deprecated