Merge pull request #18 from TRON-Bioinformatics/ubuntu-patch

Fix conda env issues on Ubuntu

Author: LKress

.gitignore

@@ -9,7 +9,7 @@ process FILTER_VCF {
     memory params.memory
     tag "${name}"
 
-    conda (params.enable_conda ? "conda-forge::libgcc-ng=10.3.0 conda-forge::gsl=2.7 bioconda::bcftools=1.15.1" : null)
+    conda (params.enable_conda ? "conda-forge::libgcc-ng=14.2.0 conda-forge::gsl=2.7 bioconda::bcftools=1.15.1" : null)
 
     input:
     	tuple val(name), file(vcf)

.gitlab-ci.yml

@@ -9,7 +9,7 @@ process BCFTOOLS_NORM {
     memory params.memory
     tag "${name}"
 
-    conda (params.enable_conda ? "conda-forge::libgcc-ng=10.3.0 conda-forge::gsl=2.7 bioconda::bcftools=1.15.1" : null)
+    conda (params.enable_conda ? "conda-forge::libgcc-ng=14.2.0 conda-forge::gsl=2.7 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 ? "conda-forge::libgcc-ng=10.3.0 conda-forge::gsl=2.7 bioconda::bcftools=1.15.1" : null)
+    conda (params.enable_conda ? "conda-forge::libgcc-ng=14.2.0 conda-forge::gsl=2.7 bioconda::bcftools=1.15.1" : null)
 
     input:
     	tuple val(name), file(vcf)

main.nf

@@ -9,7 +9,7 @@ process SUMMARY_VCF {
   tag "${name}"
   publishDir "${params.output}/${name}/metrics", mode: "copy"
 
-  conda (params.enable_conda ? "conda-forge::libgcc-ng=10.3.0 conda-forge::gsl=2.7 bioconda::bcftools=1.15.1" : null)
+  conda (params.enable_conda ? "conda-forge::libgcc-ng=14.2.0 conda-forge::gsl=2.7 bioconda::bcftools=1.15.1" : null)
 
   input:
     tuple val(name), file(vcf)

modules/01_filter.nf

@@ -12,7 +12,7 @@ process VAFATOR {
     tag "${patient_name}"
     publishDir "${params.output}/${patient_name}", mode: "copy"
 
-    conda (params.enable_conda ? "bioconda::vafator=2.2.0" : null)
+    conda (params.enable_conda ? "bioconda::vafator=2.0.3" : null)
 
     input:
     tuple val(patient_name), file(vcf), val(bams), val(purities), val(clonalities)
@@ -41,7 +41,7 @@ process MULTIALLELIC_FILTER {
     tag "${name}"
     publishDir "${params.output}/${name}", mode: "copy"
 
-    conda (params.enable_conda ? "bioconda::vafator=2.2.0" : null)
+    conda (params.enable_conda ? "bioconda::vafator=2.0.3" : null)
 
     input:
     tuple val(name), file(vcf)

modules/02_normalization.nf

@@ -36,7 +36,7 @@ process VARIANT_ANNOTATION_BCFTOOLS {
     publishDir "${params.output}/${name}", mode: "copy"
     tag "${name}"
 
-    conda (params.enable_conda ? "conda-forge::libgcc-ng=10.3.0 conda-forge::gsl=2.7 bioconda::bcftools=1.15.1" : null)
+    conda (params.enable_conda ? "conda-forge::libgcc-ng=14.2.0 conda-forge::gsl=2.7 bioconda::bcftools=1.15.1" : null)
 
     input:
         tuple val(name), file(vcf)

modules/03_summary.nf

@@ -32,7 +32,7 @@ env {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
-VERSION = '3.1.0'
+VERSION = '3.1.2'
 
 manifest {
   name = 'TRON-Bioinformatics/tronflow-vcf-postprocessing'