Develop merge for 2.3.2 release

CHANGELOG.md

@@ -4,6 +4,33 @@ 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] - 2026-03-31 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.3.2
+
+### Credits
+
+- [Magdalena Matito](https://github.com/magdasmat)
+- [Pau Pascual](https://github.com/PauPascualMas)
+- [Victor Lopez](https://github.com/victor5lm)
+
+### 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)
+- Fixed grep subtype anchor in IRMA variant-calling lablog to correctly filter Influenza B references [#644](https://github.com/BU-ISCIII/buisciii-tools/pull/644).
+- Updated assembly's RESULTS lablog in accordance to nf-core/bacass' 2.5.0 version [#645](https://github.com/BU-ISCIII/buisciii-tools/pull/645).
+
+### 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
@@ -17,7 +44,6 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - 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)
 
-
 ### Modules
 
 #### Added enhancements

buisciii/__main__.py

@@ -66,7 +66,7 @@ def run_buisciii():
         highlight=False,
     )
 
-    __version__ = "2.3.1"
+    __version__ = "2.3.2"
     stderr.print(
         "[grey39]    BUISCIII-tools version {}".format(__version__), highlight=False
     )

buisciii/templates/IRMA/ANALYSIS/ANALYSIS01_IRMA/06-variant-calling/lablog

@@ -22,7 +22,7 @@ cat ../samples_id.txt | xargs -I @@ bash -c '
     if [ -z "$subtype" ]; then
       echo "No subtype found for sample $sample. Skipping..."
     else
-      grep "$subtype" flu_type_refs.txt | cut -f 2,3 | while IFS=$'\''\t'\'' read -r fragment ref; do
+      grep "^$subtype" flu_type_refs.txt | cut -f 2,3 | while IFS=$'\''\t'\'' read -r fragment ref; do
       	if grep -qP ".*${sample}.*${fragment}" ../04-irma/all_samples_completo.txt; then
       		# for relecov
       		header_id="$(grep -P ".*${sample}.*${fragment}" ../04-irma/all_samples_completo.txt | sed "s/>//g")"

buisciii/templates/IRMA/ANALYSIS/ANALYSIS01_IRMA/lablog_versions

@@ -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\")

buisciii/templates/assembly/RESULTS/lablog_assembly_results

@@ -6,9 +6,9 @@ mkdir -p $DELIVERY_FOLDER/assembly
 cd $DELIVERY_FOLDER/assembly
 
 # Links to reports
-ln -s ../../../ANALYSIS/*ASSEMBLY/99-stats/multiqc/multiqc_report.html .
-ln -s ../../../ANALYSIS/*ASSEMBLY/99-stats/summary_assembly_metrics_mqc.csv .
-ln -s ../../../ANALYSIS/*ASSEMBLY/99-stats/kmerfinder_summary.csv .
+ln -s ../../../ANALYSIS/*ASSEMBLY/multiqc/multiqc_report.html .
+ln -s ../../../ANALYSIS/*ASSEMBLY/multiqc/summary_assembly_metrics_mqc.csv .
+ln -s ../../../ANALYSIS/*ASSEMBLY/Kmerfinder/kmerfinder_summary.csv .
 ln -s ../../../ANALYSIS/*ASSEMBLY/03-assembly/quast/global_report/report.html quast_global_report.html
 
 # Links to per reference reports

buisciii/templates/services.json

@@ -30,8 +30,8 @@
         },
         "no_copy": ["RAW", "TMP"],
         "last_folder":"REFERENCES",
-        "delivery_md": "assets/reports/md/tbprofiler_delivery.md",
-        "results_md": "assets/reports/results/tbprofiler_results.md"
+        "delivery_md": "assets/reports/md/tbprofiler.md",
+        "results_md": "assets/reports/results/tbprofiler.md"
     },
     "pikavirus": {
       "label": "Viral: Detection and characterization of viral genomes within metagenomic data",

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "buisciii-tools"
-version = "2.3.1"
+version = "2.3.2"
 dynamic = ["dependencies"]
 
 authors = [