Version history
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 indatabase.csv
(♥ to @LilyAnderssonLee for reporting, fix by @jfy133)
Fixed
- #292 - Fix Taxpasta not receiving taxonomy directory (❤️ to @SannaAb for reporting, fix by @jfy133)
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