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26 changes: 24 additions & 2 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -4,20 +4,42 @@ All notable changes to this project will be documented in this file.

The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [2.3.2_dev] - XXXX-XX-XX:

### Credits

- [Magdalena Matito](https://github.com/magdasmat)
- [Pau Pascual](https://github.com/PauPascualMas)

### Template fixes and updates

- Fixed tbprofiler `delivery_md` and `results_md` paths in `buisciii/templates/services.json` [#640](https://github.com/BU-ISCIII/buisciii-tools/pull/640)
- Fixed new taxprofiler pipeline yaml filename in versions lablog [#641](https://github.com/BU-ISCIII/buisciii-tools/pull/641)

### Modules

#### Added enhancements

#### Fixes

#### Changed

#### Removed

### Requirements

## [2.3.1] - 2026-02-26 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.3.1

### Credits

- [Pau Pascual](https://github.com/PauPascualMas)
- [Victor Lopez](https://github.com/victor5lm)
- [Magdalena Matito](https://github.com/magdasmat)

### Template fixes and updates

- Modified `create_assembly_stats.R` to group by sample in viralrecon template [#631](https://github.com/BU-ISCIII/buisciii-tools/pull/631).
- Fixed error handling in finish module and automatic logging for new_service [#632](https://github.com/BU-ISCIII/buisciii-tools/pull/632).
- Solved symlink path for TBProfiler results lablog [#634](https://github.com/BU-ISCIII/buisciii-tools/pull/634)
- Fixed tbprofiler `delivery_md` and `results_md` paths in `buisciii/templates/services.json` [#640](https://github.com/BU-ISCIII/buisciii-tools/pull/640)

### Modules

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Expand Up @@ -6,7 +6,7 @@ echo "
echo -e \${HEADER} > versions.csv

IRMA_version=\$(/data/ucct/bi/pipelines/flu-amd/flu-amd-1.2.0/IRMA | grep -o \"v[0-9]\+\.[0-9]\+\.[0-9]\+\" | head -n 1)
dehosting_method_software_version=\$(cat ../*_ANALYSIS02_TAXPROFILER/pipeline_info/nf_core_pipeline_software_mqc_versions.yml | grep \"nf-core/taxprofiler:\" | awk '{print \$NF}')
dehosting_method_software_version=\$(cat ../*_ANALYSIS02_TAXPROFILER/pipeline_info/nf_core_taxprofiler_software_mqc_versions.yml | grep \"nf-core/taxprofiler:\" | awk '{print \$NF}')
preprocessing_software_version=\$(find 02-preprocessing/ -type f -name \"*_fastp.html\" | shuf -n 1 | xargs grep -oP 'fastp version:</td><td[^>]*>\K[0-9.]+' | sed 's/^/v/')
clade_assignment_software_version=\$(find ./05-nextclade/ -type f -name \"nextclade.json\" | shuf -n 1 | xargs grep -o '\"nextcladeAlgoVersion\": *\"[^\"]*\"' | awk -F'\"' '{print \"v\"\$4}')
mafft_version=\$(find 06-variant-calling/logs/ -type f -name \"ALIGN-*\" | shuf -n 1 | xargs grep -o \"Version [0-9.]\+\" | head -n 1 | cut -d \" \" -f 2 | sed \"s/^/v/g\")
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