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#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
Deprecated
v1.1.4 - Augmented Akita Patch [2024-01-24]
Added
Fixed
#431 Updated kaiju2table module to report taxon names (fix by @Joon-Klaps)
#430 Fix the fastq output in the module LONGREAD_HOSTREMOVAL. (fix by @LilyAnderssonLee)
Dependencies
Tool
Previous version
New version
kaiju
1.8.2
1.10.0
Deprecated
v1.1.3 - Augmented Akita Patch [2024-01-12]
Added
#424 Updated to nf-core pipeline template v2.11.1 (added by @LilyAnderssonLee & @sofstam)
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
Deprecated
v1.1.1 - Augmented Akita Patch [2023-10-11]
Added
#379 Added support for previously missing Bracken-corrected Kraken2 report as output (added by @hkaspersen & @jfy133 )
#380 Updated to nf-core pipeline template v2.10 (added by @LilyAnderssonLee & @sofstam)
#393 Add validation check for a taxpasta taxonomy directory if --taxpastaadd* parameters requested (♥️ to @alimalrashed for reporting, added by @jfy133)
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)
#318New classifierMetaPhlAn4 (MetaPhlAn3 support remains) (added by @LilyAnderssonLee)
#276 Implemented batching in the KrakenUniq samples processing (added by @Midnighter)
#272 Add saving of final 'analysis-ready-reads' to dedicated directory (❤️ to @alexhbnr for request, added by @jfy133)
#303 Add support for taxpasta profile standardisation in single sample pipeline runs (❤️ to @artur-matysik for request, added by @jfy133)
#308 Add citations and bibliographic information to the MultiQC methods text of tools used in a given pipeline run (added by @jfy133)
#315 Updated to nf-core pipeline template v2.9 (added by @sofstam & @jfy133)
#321 Added support for virus hit expansion in Kaiju (❤️ to @dnlrxn for requesting, added by @jfy133)
#325 Add ability to skip sequencing quality control tools (❤️ to @vinisalazar for requesting, added by @jfy133)
#345 Add simple tutorial to explain how to get up and running with an nf-core/taxprofiler run (added by @jfy133)
#355 Add support for TAXPASTA's --add-rank-lineage to output (❤️ to @MajoroMask for request, added by @Midnighter, @sofstam, @jfy133)
#368 Add the ability to ignore profile errors caused by empty profiles and other validation errors when merging multiple profiles using TAXPASTA (added by @Midnighter and @LilyAnderssonLee)
Fixed
#271 Improved standardised table generation documentation for mOTUs manual database download tutorial (♥ to @prototaxites for reporting, fix by @jfy133)
#269 Reduced output files in AWS full test output due to very large files (fix by @jfy133)
#270 Fixed warning for host removal index parameter, and improved index checks (♥ to @prototaxites for reporting, fix by @jfy133)
#274 Substituted the samtools/bam2fq module with samtools/fastq module (fix by @sofstam)
#275 Replaced function used for error reporting to more Nextflow friendly method (fix by @jfy133)
#285 Fixed overly large log files in Kraken2 output (♥ to @prototaxites for reporting, fix by @Midnighter & @jfy133)
#286 Runtime optimisation of MultiQC step via improved log file processing (fix by @Midnighter & @jfy133)
#289 Pipeline updated to nf-core template 2.8 (fix by @Midnighter & @jfy133)
#290 Minor database input documentation improvements (♥ to @alneberg for reporting, fix by @jfy133)
#305 Fix docker/podman registry definition for tower compatibility (fix by @adamrtalbot, @jfy133)
#304 Correct mistake in kaiju2table documentation, only single rank can be supplied (♥ to @artur-matysik for reporting, fix by @jfy133)
#307 Fix databases being sometimes associated with the wrong tool (e.g. Kaiju) (fix by @jfy133, @Midnighter and @LilyAnderssonLee)
#313 Fix pipeline not providing error when database sheet does not have a header (♥ to @noah472 for reporting, fix by @jfy133)
#330 Added better tagging to allow disambiguation of Kraken2 steps of Kraken2 vs Bracken (♥ to @MajoroMask for requesting, added by @jfy133)
#334 Increase the memory of the FALCO process to 4GB (fix by @LilyAnderssonLee)
#332 Improved meta map stability for more robust pipeline resuming (fix by @jfy133)
#338 Fixed wrong file 'out' file going to centrifuge kreport module (♥ to @LilyAnderssonLee for reporting, fix by @jfy133)
#342 Fixed docs/usage to correctly list the required database files for Bracken and tips to obtain Kraken2 databases (fix by @husensofteng)
#350 Reorganize the CI tests into separate profiles in preparation for implementation of nf-test (fix by @LilyAnderssonLee)
#364 Add autoMounts to apptainer profile in nextflow.config (♥ to @hkaspersen for reporting, fix by @LilyAnderssonLee)
#372 Update modules to use quay.io nf-core mirrored containers (♥ to @maxulysse for pointing out, fix by @LilyAnderssonLee and @jfy133)
Dependencies
Tool
Previous version
New version
MultiQC
1.13
1.15
TAXPASTA
0.2.3
0.6.0
MetaPhlAn
3.0.12
4.0.6
fastp
0.23.2
0.23.4
samtools
1.16.1
1.17
Deprecated
#338 Updated Centrifuge module to not generate (undocumented) SAM alignments by default if --save_centrifuge_reads supplied, due to a Centrifuge bug modifying profile header. SAM alignments can still be generated if --out-fmt supplied in database.csv (♥ to @LilyAnderssonLee for reporting, fix by @jfy133)
v1.0.1 - Dodgy Dachshund Patch [2023-05-15]
Added
Fixed
#291 - Fix Taxpasta not receiving taxonomy directory (❤️ to @SannaAb for reporting, fix by @jfy133)
v1.0.0 - Dodgy Dachshund [2023-03-13]
Initial release of nf-core/taxprofiler, created with the nf-core template.
Add read quality control (sequencing QC, adapter removal and merging)