Modified some auxiliar viralrecon files

BU-ISCIII · Jun 18, 2024 · 79e9966 · 79e9966
1 parent b264462
commit 79e9966
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/bu_isciii/templates/viralrecon/DOC/viralrecon.config b/bu_isciii/templates/viralrecon/DOC/viralrecon.config
@@ -1,7 +1,7 @@
 singularity {
 	enabled = true
 	autoMounts = true
-        runOptions = '-B /data/bi/references/ -B /data/bi/pipelines/artic-ncov2019/artic-ncov2019/ -B "$HOME"'
+        runOptions = '-B /data/bi/references/ -B /data/bi/pipelines/artic-ncov2019/artic-ncov2019_v0/ -B "$HOME"'
 }
 
 process {

diff --git a/bu_isciii/templates/viralrecon/DOC/viralrecon_sars_nanopore.config b/bu_isciii/templates/viralrecon/DOC/viralrecon_sars_nanopore.config
@@ -1,7 +1,7 @@
 singularity {
 	enabled = true
 	autoMounts = true
-        runOptions = '-B /data/bi/references/ -B /data/bi/pipelines/artic-ncov2019/artic-ncov2019/'
+        runOptions = '-B /data/bi/references/ -B /data/bi/pipelines/artic-ncov2019/artic-ncov2019_v0/'
 }
 
 process {
@@ -10,7 +10,7 @@ process {
         withName: 'ARTIC_MINION' {
             ext.args = [
                 '--normalise 500',
-                '--scheme-directory /data/bi/pipelines/artic-ncov2019/artic-ncov2019/primer_schemes/',
+                '--scheme-directory /data/bi/pipelines/artic-ncov2019/artic-ncov2019_v0/primer_schemes/',
                 '--medaka'
             ].join(' ').trim()
         }

diff --git a/bu_isciii/templates/viralrecon/DOC/viralrecon_sars_nanopore_params.yml b/bu_isciii/templates/viralrecon/DOC/viralrecon_sars_nanopore_params.yml
@@ -2,8 +2,8 @@ platform: 'nanopore'
 protocol: 'amplicon'
 artic_scheme: 'nCoV-2019'
 primer_set_version: 5
-fasta: '/data/bi/pipelines/artic-ncov2019/artic-ncov2019/primer_schemes/nCoV-2019/V5/ESIB-EQA.reference.fasta'
-primer_bed: '/data/bi/pipelines/artic-ncov2019/artic-ncov2019/primer_schemes/nCoV-2019/V5/ESIB-EQA.primer.bed'
+fasta: '/data/bi/pipelines/artic-ncov2019/artic-ncov2019_v0/primer_schemes/nCoV-2019/V5/ESIB-EQA.reference.fasta'
+primer_bed: '/data/bi/pipelines/artic-ncov2019/artic-ncov2019_v0/primer_schemes/nCoV-2019/V5/ESIB-EQA.primer.bed'
 primer_fasta: '../../RAW/ESIB_EQA_2023.SARS1/ESIB_EQA_2023.SARS1.primers.fasta'
 kraken2_db: '/data/bi/references/eukaria/homo_sapiens/hg38/UCSC/kraken2/kraken2_human.tar.gz'
 nextclade_dataset_name: 'sars-cov-2'