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)