Skip to content

Latest commit

 

History

History
244 lines (162 loc) · 14.8 KB

CHANGELOG.md

File metadata and controls

244 lines (162 loc) · 14.8 KB
Raw

nf-core/taxprofiler: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v1.1.8 - Augmented Akita Patch [2024-06-20]

Added

  • #487 Updated to nf-core pipeline template v2.14.1 (added by @jfy133)

Fixed

  • #484 Improved input validation to immediately fail if run accession IDs within a given sample ID are not unique (❤️ to @sofstam for reporting, fixed by @jfy133)
  • #491 Added flag to publish intermediate bracken files (❤️ to @ewissel for reporting, fixed by @sofstam and @jfy133)
  • #489 Fix KrakenUniq classified reads output format mismatch (❤️ to @SannaAb for reporting, fixed by @jfy133)
  • #495 Stop TAXPASTA failures when profiles do not have exact compositionality (fixes by @Midnighter, @jfy133)

Dependencies

Tool Previous version New version
KMCP 0.9.1 0.9.4
TAXPASTA 0.6.1 0.7.0

Deprecated

  • #492 Removed --kmcp_mode parameter from KMCP to allow per database specification by setting in db_params in database sheet (fixed by @jfy133)

v1.1.7 - Augmented Akita Patch [2024-04-25]

Added

  • #477 Provide more emphasis and links to tutorials on how to retrieve and supply reference databases (❤️ to @vmkalbskopf for reporting, added by @jfy133)

Fixed

  • #476 Fixed bug in validating Bracken/Kraken/KMCP split database parameters (fixed by @LilyAnderssonLee)

Dependencies

Deprecated

v1.1.6 - Augmented Akita Patch [2024-04-16]

Added

  • #454 Updated to nf-core pipeline template v2.13.1 (added by @LilyAnderssonLee & @sofstam)
  • #461 Turned on 'strict' Nextflow evaluation runs (added by @jfy133)
  • #461 Optimised database compression so each compressed input database is untarred once, and shared amongst each run with different parameters (added by @jfy133)
  • #461 Added new parameter to optionally save uncompressed databases (added by @jfy133)
  • #471 Remove -stub run in the download_pipeline.yml because the pipeline does not support stub runs on dev (fixed by @LilyAnderssonLee)

Fixed

  • #336 Replace samplesheet check with nf-validation for both sample and database input sheets (fix by @LilyAnderssonLee)
  • #460 corrected the channel transformations to combine Kaiju and mOTUs reports with their reference databases (fix by @Midnighter)

Dependencies

Deprecated

v1.1.5 - Augmented Akita Patch [2024-02-08]

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

Tool Previous version New version
Centrifuge 1.0.4_beta 1.0.4.1

Deprecated

v1.1.4 - Augmented Akita Patch [2024-01-24]

Added

Fixed

  • #431 Updated kaiju2table module to report taxon names (fix by @Joon-Klaps)
  • #430 Fix the fastq output in the module LONGREAD_HOSTREMOVAL. (fix by @LilyAnderssonLee)

Dependencies

Tool Previous version New version
kaiju 1.8.2 1.10.0

Deprecated

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

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

Deprecated

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

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)
  • #321 Added support for virus hit expansion in Kaiju (❤️ to @dnlrxn for requesting, added by @jfy133)
  • #325 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 @hkaspersen 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)

v1.0.1 - Dodgy Dachshund Patch [2023-05-15]

Added

Fixed

  • #291 - Fix Taxpasta not receiving taxonomy directory (❤️ to @SannaAb for reporting, fix by @jfy133)

v1.0.0 - Dodgy Dachshund [2023-03-13]

Initial release of nf-core/taxprofiler, created with the nf-core template.

  • 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

Added

Fixed

Dependencies

Deprecated