Releases: nf-core/taxprofiler
Releases · nf-core/taxprofiler
v1.1.2 - Augmented Akita Patch [2023-10-27]
Added
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
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
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-lineageto 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
-
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li>#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 kreportmodule (♥ 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-fmtsupplied indatabase.csv(♥ to @LilyAnderssonLee for reporting, fix by @jfy133)
Contributors
Midnighter, maxulysse, and 13 other contributors
Assets 2
v1.0.1 - Dodgy Dachshund Patch [2023-05-15]
Contributors
jfy133 and SannaAb
Assets 2
v1.0.0 - Dodgy Dachshund [2023-03-13]
v1.0.0 - Dodgy Dachshund [2023-03-13]
Added
- Add read quality control (sequencing QC, adapter removal and merging)
- Add read complexity filtering
- Add host-reads removal step
- Add run merging
- Add taxonomic classification
- Add taxon table standardisation
- Add post-classification visualisation
Contributed by: @jfy133 @sofstam @Midnighter @ljmesi @MillironX @jianhong @mjamy @rafalstepien @maxibor @talnor
Contributors
Midnighter, jianhong, and 8 other contributors