Add libgcc with v14.2.0 to conda environments

TRON-Bioinformatics · Jan 9, 2025 · f30e284 · f30e284
1 parent 3aef48d
commit f30e284
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Showing 4 changed files with 5 additions and 5 deletions.
diff --git a/modules/01_filter.nf b/modules/01_filter.nf
@@ -9,7 +9,7 @@ process FILTER_VCF {
     memory params.memory
     tag "${name}"
 
-    conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
+    conda (params.enable_conda ? "conda-forge::libgcc-ng=14.2.0 bioconda::bcftools=1.15.1" : null)
 
     input:
     	tuple val(name), file(vcf)

diff --git a/modules/02_normalization.nf b/modules/02_normalization.nf
@@ -9,7 +9,7 @@ process BCFTOOLS_NORM {
     memory params.memory
     tag "${name}"
 
-    conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
+    conda (params.enable_conda ? "conda-forge::libgcc-ng=14.2.0 bioconda::bcftools=1.15.1" : null)
 
     input:
     	tuple val(name), file(vcf)
@@ -54,7 +54,7 @@ process REMOVE_DUPLICATES {
     tag "${name}"
     publishDir "${params.output}/${name}", mode: "copy"
 
-    conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
+    conda (params.enable_conda ? "conda-forge::libgcc-ng=14.2.0 bioconda::bcftools=1.15.1" : null)
 
     input:
     	tuple val(name), file(vcf)

diff --git a/modules/03_summary.nf b/modules/03_summary.nf
@@ -9,7 +9,7 @@ process SUMMARY_VCF {
   tag "${name}"
   publishDir "${params.output}/${name}/metrics", mode: "copy"
 
-  conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
+  conda (params.enable_conda ? "conda-forge::libgcc-ng=14.2.0 bioconda::bcftools=1.15.1" : null)
 
   input:
     tuple val(name), file(vcf)

diff --git a/modules/06_variant_annotation.nf b/modules/06_variant_annotation.nf
@@ -36,7 +36,7 @@ process VARIANT_ANNOTATION_BCFTOOLS {
     publishDir "${params.output}/${name}", mode: "copy"
     tag "${name}"
 
-    conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
+    conda (params.enable_conda ? "conda-forge::libgcc-ng=14.2.0 bioconda::bcftools=1.15.1" : null)
 
     input:
         tuple val(name), file(vcf)