Version 1.0.0-rc10

ℹ️ This is a release candidate for the first production release (v1.0.0) of the GPS Pipeline
ℹ️ This version of the pipeline has been validated by 500 random samples from the GPS Database

What's Changed (since v1.0.0-rc9)

Changes

• Update PopPUNK Database to GPS v9 (#114): Enable the pipeline to assign GPSCs to more samples
• .refs is no longer required for PopPUNK database (#115): Allow the pipeline to use PopPUNK database without reference-only data
• Update mlst image with MLST database built in 2024 July (#117): Enable the pipline to assign MLSTs to more samples
• Update bundled Nextflow to 24.04.4 (http://github.com/sanger-bentley-group/gps-pipeline/pull/118)

Full Changelog: v1.0.0-rc9...v1.0.0-rc10

Version 1.0.0-rc9

ℹ️ This is a release candidate for the first production release (v1.0.0) of the GPS Pipeline
ℹ️ This version of the pipeline has been validated by 500 random samples from the GPS Database

What's Changed (since v1.0.0-rc8)

Changes

• Switch to Docker Compose v2 (#110): Docker Compose v1 was deprecated on 2023 June 30, migrated to Docker Compose v2 in --init to ensure compatibility with current and future Docker versions

Fixes

• Fix minor issues in ARIBA database and logic (#109): Fixed incorrect target names and improved folP detection logic to ensure accurate AMR prediction

Full Changelog: v1.0.0-rc8...v1.0.0-rc9

Version 1.0.0-rc8

ℹ️ This is a release candidate for the first production release (v1.0.0) of the GPS Pipeline
ℹ️ This version of the pipeline has been validated by 500 random samples from the GPS Database

What's Changed (since v1.0.0-rc7)

New Features

• Save actual assembler thread count when all available are used (#104): The thread count available to the assembler container will be saved to info.txt if the user does not specify a thread count, instead of just stating 0

Changes

• Use workflow.container introspection to acquire image/container information (#101): Ensure acquiring accurate image/container information. Bumped the minimum required version of Nextflow to v23.10.0

• Update bundled Nextflow executable to 24.04.2 (#105)

Fixes

• Fix empty unpaired reads crashing Unicycler (#102): In the event of an empty unpaired read is generated by fastp, it will not be used by Unicycler to prevent the tool from crashing
• Changed the version matching operator (#103): Nextflow developers have updated the documentation on version matching operator, changed to a more appropiate operator based on the update

Full Changelog: v1.0.0-rc7...v1.0.0-rc8

Version 1.0.0-rc7

ℹ️ This is a release candidate for the first production release (v1.0.0) of the GPS Pipeline
ℹ️ This version of the pipeline has been validated by 500 random samples from the GPS Database

What's Changed (since v1.0.0-rc6)

Fixes

• Fixing GPSC assignment for samples with dot in filename (#98): GPSC can now be correctly assigned to samples with dot in their filenames

Full Changelog: v1.0.0-rc6...v1.0.0-rc7

Version 1.0.0-rc6

ℹ️ This is a release candidate for the first production release (v1.0.0) of the GPS Pipeline
ℹ️ This version of the pipeline has been validated by 500 random samples from the GPS Database

What's Changed (since v1.0.0-rc5)

Fixes

• Proper 23s rRNA mutation-based ERY+CLI resistance detection (#96): The pipeline can now correctly detect ERY and CLI resistance caused by 23s rRNA A2061G mutation

Changes

• Update README.md: Added links to installation guides for software dependencies; corrected issue in the workflow chart

Full Changelog: v1.0.0-rc5...v1.0.0-rc6

Version 1.0.0-rc5

ℹ️ This is a release candidate for the first production release (v1.0.0) of the GPS Pipeline
ℹ️ This version of the pipeline has been validated by 500 random samples from the GPS Database

What's Changed (since v1.0.0-rc4)

New Features

• Allow optional assembler thread count option (#93): Allow users to optionally specify the number of threads used by the assembler via --assembler_thread. As SPAdes-based assembler is deterministic for a given count of threads, this option enables reproducible assemblies generation.

Changes

• Update SeroBA and its database to v1.0.7 (#92)

Known Issues

• The ARIBA-based non-PBP AMR detection cannot reliably detect AMR caused by 23S rRNA mutations

Full Changelog: v1.0.0-rc4...v1.0.0-rc5

Version 1.0.0-rc4

ℹ️ This is a release candidate for the first production release (v1.0.0) of the GPS Pipeline
ℹ️ This version of the pipeline has been validated by 500 random samples from the GPS Database

What's Changed (since v1.0.0-rc3)

Fixes

• Input File Validation (#90): Corrupted input files no longer crash the pipeline. The pipeline will indicate which read file is detected to be corrupted.

Known Issues

• The ARIBA-based non-PBP AMR detection cannot reliably detect AMR caused by 23S rRNA mutations

Full Changelog: v1.0.0-rc3...v1.0.0-rc4

Version 1.0.0-rc3

What's Changed

ℹ️ This is a release candidate for the first production release (v1.0.0) of the GPS Pipeline
ℹ️ This version of the pipeline has been validated by 500 random samples from the GPS Database

What's Changed (since v1.0.0-rc2)

New Features

• Inferred Minimum Inhibitory Concentration (MIC) range of other AMR (#84): The results.csv now includes inferred MIC range of some of the antimicrobial in "Other AMR" type based on 2014 CLSI guidelines by default.

Changes

• Change name to GPS Pipeline from GPS Unified Pipeline (#83): The pipeline is now called GPS Pipeline and its repository has transferred to sanger-bentley-group
• Update PopPUNK database to GPS v8 (reference only) database (#85): Updating to GPS v8 (reference only) database for PopPUNK. It reduces the total database size from 30GB to 8GB.

Fixes

• Proper implementation of dynamic retry directive (#86)

Known Issues

• The ARIBA-based non-PBP AMR detection cannot reliably detect AMR caused by 23S rRNA mutations

Full Changelog: v1.0.0-rc2...v1.0.0-rc3

Version 1.0.0-rc2

ℹ️ This is a release candidate for the first production release (v1.0.0) of the GPS Unified Pipeline
ℹ️ This version of the pipeline has been validated by 500 random samples from the GPS Database

What's Changed (since v1.0.0-rc1)

Changes

• Optional test input (#81): Test input data is now an optional download via download_test_input to reduce the size of the repository and releases

Fixes

• Fix: ref_start and ref_end could be non-numeric (#80): Bug fix for parse_other_resistance.pywhen a folP line in the ARIBA report contains non-numeric value in either ref_start or ref_end column

Known Issues

• The ARIBA-based non-PBP AMR detection cannot reliably detect AMR caused by 23S rRNA mutations

Full Changelog: v1.0.0-rc1...v1.0.0-rc2

Version 1.0.0-rc1

ℹ️ This is a release candidate for the first production release (v1.0.0) of the GPS Unified Pipeline
ℹ️ This version of the pipeline has been validated by 500 random samples from the GPS Database

What's Changed

New Features

• Non-PBP AMR detection rewrite (#57, #67, #71, #73, #79)
  • Non-PBP AMR detection is rewritten to be based on ARIBA and a custom Python script instead of AMRSearch
• Additional Taxonomy QC parameter: Maximum non-Streptococcus genus percentage in reads (#75)
  • The non-Streptococcus genus percentage in reads is now also part of the Taxonomy QC (default is ≤ 2.00%)
  • results.csv now include information on the most abundant non-Streptococcus genus in reads and its percentage
• Nextflow Tower Support (#63, #66, #68)
  • The pipeline can now be launched directly from Nextflow Tower Launchpad (in addition to monitoring on Nextflow Tower using -with-tower)
  • This feature has only been tested on Sanger farm5 HPC. You will need to provide your own Nextflow Config profile when working on other Compute Environments.

Changes

• Databases handling improvements (#57, #64, #74)
  • SeroBA database source files are now based on versioned releases instead of the latest version
  • All databases are now saved in subdirectories of a single directory
  • Improve the robustness of the database saving mechanism
  • Run checksum on locally provided files to ensure generated databases are up-to-date
• Revamp output logic and other code improvements (#58, #72)
  • Improve robustness of the results output logic and is now executed as a Python script
  • Shell scripts code style improvements
• Improve robustness of LSF profile (#61)
• Unify relational operators in QC parameters (#76)
• Update the default mlst image to staphb/mlst:2.23.0-2023-07 (#62)
• Update the default fastp image to staphb/fastp:0.23.4 (#62)
• Update the default spn-pbp-amr image to sangerbentleygroup/spn-pbp-amr:23.10.2 (#74)
• Update the default SeroBA image to sangerbentleygroup/seroba:1.0.5 (#77)
• Update the included Nextflow Executable to 23.10.0 (#70)

Fixes

• Fix error when Nextflow tries to collect metrics in Python container (#59)
• Add missing process labels to GET_KRAKEN2_DB (#69)

Known Issues

• The ARIBA-based non-PBP AMR detection cannot reliably detect AMR caused by 23S rRNA mutations

Full Changelog: v0.8.2-beta...v1.0.0-rc1