Releases · nf-core/taxprofiler

12 Jan 15:15

jfy133

1.1.3

df4e001

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

Contributors

Midnighter, mashehu, and 4 other contributors

Assets 2

27 Oct 09:31

jfy133

1.1.2

3d4eda2

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

Contributors

jfy133 and MajoroMask

Assets 2

11 Oct 13:36

LilyAnderssonLee

1.1.1

baede5b

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)

`Dependencies`

Tool	Previous version	New version
KrakenUniq	1.0.2	1.0.4
taxpasta	0.6.0	0.6.1

`Deprecated`

Contributors

Midnighter, asafpr, and 6 other contributors

Assets 2

19 Sep 05:51

LilyAnderssonLee

1.1.0

d1f82f3

v1.1.0 - Augmented Akita [2023-09-19]

`Added`

#298 New classifier ganon (added by @jfy133)
#312 New classifier KMCP (added by @sofstam)
#318 New classifier MetaPhlAn4 (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)
#319 Added support for virus hit expansion in Kaiju (❤️ to @dnlrxn for requesting, added by @jfy133)
#323 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 @hkaspersento 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)