Version history

Added

  • #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

ToolPrevious versionNew version
Centrifuge1.0.4_beta1.0.4.1

Fixed

Dependencies

ToolPrevious versionNew version
kaiju1.8.21.10.0

Added

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

ToolPrevious versionNew version
multiqc1.151.19
fastqc11.912.1
nf-validationunpinned1.1.3

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

ToolPrevious versionNew version
megan/rma2info6.21.76.24.20

Added

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

ToolPrevious versionNew version
KrakenUniq1.0.21.0.4
taxpasta0.6.00.6.1

Deprecated

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

ToolPrevious versionNew version
MultiQC1.131.15
TAXPASTA0.2.30.6.0
MetaPhlAn3.0.124.0.6
fastp0.23.20.23.4
samtools1.16.11.17

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)

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