BU-ISCIII · victor5lm · Jun 22, 2026 · Jun 23, 2026 · Jun 23, 2026 · Jul 1, 2026
diff --git a/.github/workflows/python_lint.yml b/.github/workflows/python_lint.yml
@@ -4,7 +4,7 @@ on:
   push:
     branches: "**"
   pull_request:
-    types: [opened, reopened, synchronize, closed]
+    types: [opened, reopened, synchronize]
     branches: "**"
 
 jobs:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,37 @@ 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).
 
+## [2.3.4] - 2026-07-02 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.3.4
+
+### Credits
+
+- [Enrique Sapena](https://github.com/ESapenaVentura)
+- [Victor Lopez](https://github.com/victor5lm)
+
+### Template fixes and updates
+
+- Updated assembly config for MultiQC and RESULTS lablog [#708](https://github.com/BU-ISCIII/buisciii-tools/pull/708)
+- Updated iGenomes paths [#710](https://github.com/BU-ISCIII/buisciii-tools/pull/710)
+- Updated the assembly template to skip busco and some paths in correspondence to refgenie system [#711](https://github.com/BU-ISCIII/buisciii-tools/pull/711)
+
+### Modules
+
+#### Implementation
+
+#### Added enhancements
+
+#### Fixes
+
+- Fixed local file access for PDF generation via wkhtmltopdf [#705](https://github.com/BU-ISCIII/buisciii-tools/pull/705)
+
+#### Changed
+
+#### Removed
+
+### Requirements
+
+- Updated wkhtmltopdf version requirement from 0.12.4 to 0.12.6.1 [#708](https://github.com/BU-ISCIII/buisciii-tools/pull/708)
+
 ## [2.3.3] - 2026-06-22 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.3.3
 
 ### Credits

diff --git a/buisciii/__main__.py b/buisciii/__main__.py
@@ -66,7 +66,7 @@ def run_buisciii():
         highlight=False,
     )
 
-    __version__ = "2.3.3"
+    __version__ = "2.3.4"
     stderr.print(
         "[grey39]    BUISCIII-tools version {}".format(__version__), highlight=False
     )

diff --git a/buisciii/bioinfo_doc.py b/buisciii/bioinfo_doc.py
@@ -552,7 +552,10 @@ def convert_to_pdf(self, html_file):
         pdf_file = html_file.replace(".html", ".pdf")
         try:
             pdfkit.from_file(
-                html_file, output_path=pdf_file, configuration=self.config_pdfkit
+                html_file,
+                output_path=pdf_file,
+                configuration=self.config_pdfkit,
+                options={"enable-local-file-access": ""},
             )
             log.info(f"PDF file created successfully: {pdf_file}")
         except OSError as e:

diff --git a/buisciii/templates/DROP/ANALYSIS/DATE_ANALYSIS01_DROP/AberrantExpression/config.yaml b/buisciii/templates/DROP/ANALYSIS/DATE_ANALYSIS01_DROP/AberrantExpression/config.yaml
@@ -9,7 +9,7 @@ sampleAnnotation: sample_annotation_AE.tsv
 geneAnnotation:
     gencode29: /data/ucct/bi/references/refgenie/alias/hg19/gtf/gencode29/gencode.v29lift37.annotation.gtf
 genomeAssembly: hg19
-genome: /data/ucct/bi/references/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa
+genome: /data/ucct/bi/references/refgenie/alias/Homo_sapiens_Ensembl_GRCh37/fasta/v20230419/genome.fa
     # You can define multiple reference genomes in yaml format, ncbi: path/to/ncbi, ucsc: path/to/ucsc
     # the keywords that define the path should be in the GENOME column of the sample annotation table
 

diff --git a/buisciii/templates/DROP/ANALYSIS/DATE_ANALYSIS01_DROP/AberrantSplicing/config.yaml b/buisciii/templates/DROP/ANALYSIS/DATE_ANALYSIS01_DROP/AberrantSplicing/config.yaml
@@ -9,7 +9,7 @@ sampleAnnotation: sample_annotation_AS.tsv
 geneAnnotation:
     gencode29: /data/ucct/bi/references/refgenie/alias/hg19/gtf/gencode29/gencode.v29lift37.annotation.gtf
 genomeAssembly: hg19
-genome: /data/ucct/bi/references/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa
+genome: /data/ucct/bi/references/refgenie/alias/Homo_sapiens_Ensembl_GRCh37/fasta/v20230419/genome.fa
     # You can define multiple reference genomes in yaml format, ncbi: path/to/ncbi, ucsc: path/to/ucsc
     # the keywords that define the path should be in the GENOME column of the sample annotation table
 

diff --git a/buisciii/templates/DROP/ANALYSIS/DATE_ANALYSIS01_DROP/MAE/config.yaml b/buisciii/templates/DROP/ANALYSIS/DATE_ANALYSIS01_DROP/MAE/config.yaml
@@ -9,7 +9,7 @@ sampleAnnotation: sample_annotation_MAE.tsv
 geneAnnotation:
     gencode29: /data/ucct/bi/references/refgenie/alias/hg19/gtf/gencode29/gencode.v29lift37.annotation.gtf
 genomeAssembly: hg19
-genome: /data/ucct/bi/references/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa
+genome: /data/ucct/bi/references/refgenie/alias/Homo_sapiens_Ensembl_GRCh37/fasta/v20230419/genome.fa
     # You can define multiple reference genomes in yaml format, ncbi: path/to/ncbi, ucsc: path/to/ucsc
     # the keywords that define the path should be in the GENOME column of the sample annotation table
 

diff --git a/buisciii/templates/assembly/ANALYSIS/ANALYSIS01_ASSEMBLY/lablog b/buisciii/templates/assembly/ANALYSIS/ANALYSIS01_ASSEMBLY/lablog
@@ -123,6 +123,7 @@ nextflow run /data/ucct/bi/pipelines/nf-core-bacass/nf-core-bacass-2.5.0/main.nf
         --save_trimmed ${SAVETRIMMED} \\
         --skip_kraken2 true \\
         --skip_kmerfinder false \\
+        --skip_busco true \\
         --kmerfinderdb /data/ucct/bi/references/kmerfinder/latest/bacteria \\
         --ncbi_assembly_metadata /data/ucct/bi/references/bacteria/20240626/assembly_summary_refseq.txt \\
         ${PROKKA_ARGS} \\

diff --git a/buisciii/templates/assembly/DOC/hpc_slurm_assembly.config b/buisciii/templates/assembly/DOC/hpc_slurm_assembly.config
@@ -221,7 +221,8 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-    withName: 'MULTIQC_CUSTOM' {
+    withName: 'CUSTOM_MULTIQC' {
+        ext.args = '--interactive'
         publishDir = [
             [ 
                 path: { "${params.outdir}/99-stats/multiqc" },

diff --git a/buisciii/templates/assembly/RESULTS/lablog_assembly_results b/buisciii/templates/assembly/RESULTS/lablog_assembly_results
@@ -6,8 +6,8 @@ mkdir -p $DELIVERY_FOLDER/assembly
 cd $DELIVERY_FOLDER/assembly
 
 # Links to reports
-ln -s ../../../ANALYSIS/*ASSEMBLY/multiqc/multiqc_report.html .
-ln -s ../../../ANALYSIS/*ASSEMBLY/multiqc/summary_assembly_metrics_mqc.csv .
+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/Kmerfinder/kmerfinder_summary.csv .
 ln -s ../../../ANALYSIS/*ASSEMBLY/03-assembly/quast/global_report/report.html quast_global_report.html
 

diff --git a/buisciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/lablog b/buisciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/lablog
@@ -1,3 +1,3 @@
 # module load singularity
 
-cp /data/ucct/bi/references/ariba/databases.txt .
+cp /data/ucct/bi/references/refgenie/alias/ariba/databases.txt .
diff --git a/buisciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/05-mlva/lablog b/buisciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/05-mlva/lablog
@@ -6,7 +6,7 @@ mkdir MLVA_output
 scratch_dir=$(pwd | sed 's|/data/ucct/bi/scratch_tmp|/scratch|g')
 cp ../../*_ASSEMBLY/03-assembly/unicycler/*.fasta* assemblies/
 gzip -d assemblies/*.fasta.gz
-available_primers=$(ls /data/ucct/bi/references/MLVA/*primer* | rev | cut -d "/" -f1 | rev | cut -d "_" -f1)
+available_primers=$(ls /data/ucct/bi/references/refgenie/alias/MLVA/primers/v20231004/*primer* | rev | cut -d "/" -f1 | rev | cut -d "_" -f1)
 
 echo "Available primers:"
 select primer in $available_primers; do
@@ -18,6 +18,6 @@ select primer in $available_primers; do
     fi
 done
 
-primer_file=$(ls /data/ucct/bi/references/MLVA/${primer}*)
+primer_file=$(ls /data/ucct/bi/references/refgenie/alias/MLVA/primers/v20231004/${primer}*)
 
 echo "srun --partition short_idx --chdir ${scratch_dir} --output logs/MLVA.log --job-name MLVA python /data/ucct/bi/pipelines/mlva/MLVA_finder.py -c -i assemblies -o MLVA_output -p ${primer_file} --full-locus-name --predicted-PCR-size-table --flanking-seq 20 &"  > _01_mlva.sh
diff --git a/buisciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/lablog b/buisciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/lablog
@@ -38,7 +38,7 @@ nextflow run /data/ucct/bi/pipelines/nf-core-sarek/nf-core-sarek_3.4.4/3_4_4/mai
 	--dbsnp '/data/ucct/bi/references/eukaria/homo_sapiens/hg19/1000genomes_b37/variants/20131208/dbsnp_138_mod.b37.vcf.gz' \\
 	--dbsnp_tbi '/data/ucct/bi/references/eukaria/homo_sapiens/hg19/1000genomes_b37/variants/20131208/dbsnp_138_mod.b37.vcf.gz.tbi' \\
 	--igenomes_ignore \\
-	--igenomes_base '/data/ucct/bi/references/igenomes/' \\
+	--igenomes_base '/data/ucct/bi/references/refgenie/alias/' \\
 	--tools 'haplotypecaller' \\
 	--joint_germline \\
 	-resume

diff --git a/buisciii/templates/exomeeb/DOC/hpc_slurm_sarek.config b/buisciii/templates/exomeeb/DOC/hpc_slurm_sarek.config
@@ -26,23 +26,23 @@ params {
 	max_time = '48.h'
 	genomes {
 	'GATK.GRCh37' {
-		ascat_alleles         = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/G1000_alleles_hg19.zip"
+		ascat_alleles         = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/annotation-ASCAT/v20230419/G1000_alleles_hg19.zip"
 		ascat_genome          = 'hg19'
-		ascat_loci            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/G1000_loci_hg19.zip"
-		ascat_loci_gc         = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/GC_G1000_hg19.zip"
-		ascat_loci_rt         = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/RT_G1000_hg19.zip"
-		bwa                   = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/"
-		chr_dir               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/Chromosomes"
-		dict                  = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.dict"
-		fasta                 = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta"
-		fasta_fai             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta.fai"
-		germline_resource     = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/af-only-gnomad.raw.sites.vcf.gz"
-		germline_resource_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/af-only-gnomad.raw.sites.vcf.gz.tbi"
-		intervals             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/intervals/wgs_calling_regions_Sarek.list"
-		known_snps            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/1000G_phase1.snps.high_confidence.b37.vcf.gz"
-		known_snps_tbi        = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/1000G_phase1.snps.high_confidence.b37.vcf.gz.tbi"
-		known_indels          = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.gz"
-		known_indels_tbi      = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.gz.tbi"
+		ascat_loci            = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/annotation-ASCAT/v20230419/G1000_loci_hg19.zip"
+		ascat_loci_gc         = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/annotation-ASCAT/v20230419/GC_G1000_hg19.zip"
+		ascat_loci_rt         = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/annotation-ASCAT/v20230419/RT_G1000_hg19.zip"
+		bwa                   = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/bwa_index/v20230419/"
+		chr_dir               = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/chromosomes/v20230419/"
+		dict                  = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/fasta/v20230419/human_g1k_v37_decoy.dict"
+		fasta                 = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/fasta/v20230419/human_g1k_v37_decoy.fasta"
+		fasta_fai             = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/fasta/v20230419/human_g1k_v37_decoy.fasta.fai"
+		germline_resource     = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/annotation-GATKBundle/v20230419/af-only-gnomad.raw.sites.vcf.gz"
+		germline_resource_tbi = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/annotation-GATKBundle/v20230419/af-only-gnomad.raw.sites.vcf.gz.tbi"
+		intervals             = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/annotation-intervals/v20230419/wgs_calling_regions_Sarek.list"
+		known_snps            = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/annotation-GATKBundle/v20230419/1000G_phase1.snps.high_confidence.b37.vcf.gz"
+		known_snps_tbi        = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/annotation-GATKBundle/v20230419/1000G_phase1.snps.high_confidence.b37.vcf.gz.tbi"
+		known_indels          = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/annotation-GATKBundle/v20230419/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.gz"
+		known_indels_tbi      = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/annotation-GATKBundle/v20230419/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.gz.tbi"
 		snpeff_db             = 'GRCh37.87'
 		snpeff_genome         = 'GRCh37'
 		snpeff_version        = '5.1'

diff --git a/buisciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/lablog b/buisciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/lablog
@@ -58,7 +58,7 @@ nextflow run /data/ucct/bi/pipelines/nf-core-sarek/nf-core-sarek_3.4.4/3_4_4/mai
           --save_reference \\
           --joint_germline \\
 		  --igenomes_ignore \\
-		  --igenomes_base '/data/ucct/bi/references/igenomes/' \\
+		  --igenomes_base '/data/ucct/bi/references/refgenie/alias/' \\
 	  	  -resume
 EOF
 

diff --git a/buisciii/templates/exometrio/DOC/hpc_slurm_sarek.config b/buisciii/templates/exometrio/DOC/hpc_slurm_sarek.config
@@ -26,23 +26,23 @@ params {
 	max_time = '48.h'
 	genomes {
 	'GATK.GRCh37' {
-		ascat_alleles         = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/G1000_alleles_hg19.zip"
+		ascat_alleles         = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/annotation-ASCAT/v20230419/G1000_alleles_hg19.zip"
 		ascat_genome          = 'hg19'
-		ascat_loci            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/G1000_loci_hg19.zip"
-		ascat_loci_gc         = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/GC_G1000_hg19.zip"
-		ascat_loci_rt         = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/RT_G1000_hg19.zip"
-		bwa                   = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/"
-		chr_dir               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/Chromosomes"
-		dict                  = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.dict"
-		fasta                 = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta"
-		fasta_fai             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta.fai"
-		germline_resource     = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/af-only-gnomad.raw.sites.vcf.gz"
-		germline_resource_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/af-only-gnomad.raw.sites.vcf.gz.tbi"
-		intervals             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/intervals/wgs_calling_regions_Sarek.list"
-		known_snps            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/1000G_phase1.snps.high_confidence.b37.vcf.gz"
-		known_snps_tbi        = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/1000G_phase1.snps.high_confidence.b37.vcf.gz.tbi"
-		known_indels          = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.gz"
-		known_indels_tbi      = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.gz.tbi"
+		ascat_loci            = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/annotation-ASCAT/v20230419/G1000_loci_hg19.zip"
+		ascat_loci_gc         = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/annotation-ASCAT/v20230419/GC_G1000_hg19.zip"
+		ascat_loci_rt         = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/annotation-ASCAT/v20230419/RT_G1000_hg19.zip"
+		bwa                   = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/bwa_index/v20230419/"
+		chr_dir               = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/chromosomes/v20230419/"
+		dict                  = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/fasta/v20230419/human_g1k_v37_decoy.dict"
+		fasta                 = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/fasta/v20230419/human_g1k_v37_decoy.fasta"
+		fasta_fai             = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/fasta/v20230419/human_g1k_v37_decoy.fasta.fai"
+		germline_resource     = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/annotation-GATKBundle/v20230419/af-only-gnomad.raw.sites.vcf.gz"
+		germline_resource_tbi = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/annotation-GATKBundle/v20230419/af-only-gnomad.raw.sites.vcf.gz.tbi"
+		intervals             = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/annotation-intervals/v20230419/wgs_calling_regions_Sarek.list"
+		known_snps            = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/annotation-GATKBundle/v20230419/1000G_phase1.snps.high_confidence.b37.vcf.gz"
+		known_snps_tbi        = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/annotation-GATKBundle/v20230419/1000G_phase1.snps.high_confidence.b37.vcf.gz.tbi"
+		known_indels          = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/annotation-GATKBundle/v20230419/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.gz"
+		known_indels_tbi      = "${params.igenomes_base}/Homo_sapiens_GATK_GRCh37/annotation-GATKBundle/v20230419/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.gz.tbi"
 		snpeff_db             = 'GRCh37.87'
 		snpeff_genome         = 'GRCh37'
 		snpeff_version        = '5.1'

diff --git a/buisciii/templates/pikavirus/DOC/hpc_slurm_pikavirus.config b/buisciii/templates/pikavirus/DOC/hpc_slurm_pikavirus.config
@@ -10,7 +10,7 @@ process {
 params {
   config_profile_name = 'ISCIII HPC profile'
   config_profile_description = 'Profile designed for the High Performance Computer in the ISCIII'
-  kraken2_db = "/data/ucct/bi/references/kraken/minikraken_8GB_20200312"
+  kraken2_db = "/data/ucct/bi/references/refgenie/alias/kraken/minikraken_8GB/v20200312"
   vir_ref_dir = "/data/ucct/bi/references/PikaVirus/viral_assemblies_for_pikavirus"
   vir_dir_repo = "/data/ucct/bi/references/PikaVirus/viral_assemblies.tsv"
   bact_ref_dir = "/data/ucct/bi/references/PikaVirus/bacteria_assemblies_for_pikavirus"

diff --git a/buisciii/templates/viralrecon/DOC/viralrecon_sars_nanopore.config b/buisciii/templates/viralrecon/DOC/viralrecon_sars_nanopore.config
@@ -10,7 +10,7 @@ process {
         withName: 'ARTIC_MINION' {
             ext.args = [
                 '--normalise 500',
-                '--scheme-directory /data/ucct/bi/references/virus/2019-nCoV/primer_schemes/',
+                '--scheme-directory /data/ucct/bi/references/refgenie/alias/coronaviridae/primer_schemes/',
                 '--medaka'
             ].join(' ').trim()
         }

diff --git a/buisciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/lablog b/buisciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/lablog
@@ -52,7 +52,7 @@ nextflow run /data/ucct/bi/pipelines/nf-core-sarek/nf-core-sarek_3.4.4/3_4_4/mai
           --dbsnp '/data/ucct/bi/references/eukaria/homo_sapiens/hg19/1000genomes_b37/variants/20131208/dbsnp_138_mod.b37.vcf.gz' \\
               --dbsnp_tbi '/data/ucct/bi/references/eukaria/homo_sapiens/hg19/1000genomes_b37/variants/20131208/dbsnp_138_mod.b37.vcf.gz.tbi' \\
               --igenomes_ignore \\
-              --igenomes_base '/data/ucct/bi/references/igenomes/' \\
+              --igenomes_base '/data/ucct/bi/references/refgenie/alias/' \\
               --tools 'haplotypecaller' \\
           --joint_germline \\
                   -resume