v1.0.0-rc12

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 21K samples from the GPS Database published data

The GPS Pipeline is now in preprint! 🎉
Please cite this pipeline if you have used it in your work: https://doi.org/10.1101/2024.11.27.625679 [Preprint]

What's Changed (since v1.0.0-rc11)

Changes

• Update to SeroBA 2.0.4 (#137): Predict 102 of 107 known pneumococcal serotypes, 16 subtypes in selected serotypes, and 4 groups of non-encapsulated pneumococci
• Update Nextflow to 24.10.3 (#140): Compatible with the latest version of Nextflow

Fixes

• Fail the PBP_RESISTANCE process if spn_pbp_amr generates empty output (#138): As spn_pbp_amr should not generate empty output, the process will be properly considered as fail if it does.
• Cap maximum thread usage to samtools sort due to diminishing return and to avoid excessive memory request (#139): As samtools sort assigns memory per thread and there is a diminishing return beyond 8 threads, it will no longer use more than 8 threads to avoid edge cases where a machine has high thread count but only limited memory available crashing the tool

Full Changelog: v1.0.0-rc11...v1.0.0-rc12

v1.0.0-rc11

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 21K samples from the GPS Database published data

The GPS Pipeline is now in preprint! 🎉
Please cite this pipeline if you have used it in your work: https://doi.org/10.1101/2024.11.27.625679 [Preprint]

What's Changed (since v1.0.0-rc10)

New Features

• Implementation of graceful failure (#127, #129, #130, #133): The failure of an individual module should no longer crash the entire pipeline

Changes

• Improve documentation (#121, #126, #128, #131, #132): Easier on the eyes and more accurate
• Update repo URL after organisation transfer (#123): The repository of the GPS Pipeline has moved from sanger-bentley-group/gps-pipeline to GlobalPneumoSeq/gps-pipeline

Fixes

• Ensure gene name is always in the first portion of the ref_name (#125): No more guesswork about the gene name in the ref_name

Full Changelog: v1.0.0-rc10...v1.0.0-rc11

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