SNP_calling.config: fix module load for SGE

src/SNP_calling.config

@@ -52,7 +52,8 @@ profiles {
       queueSize = 1000
       pollInterval = '60sec'
       withName: adaptor_removal {
-        beforeScript = "module purge; module load cutadapt/1.14"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "cutadapt/1.14"
         executor = "sge"
         cpus = 1
         memory = "20GB"
@@ -60,7 +61,8 @@ profiles {
         queue = 'monointeldeb128'
       }
       withName: trimming {
-        beforeScript = "module purge; module load UrQt/d62c1f8"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "UrQt/d62c1f8"
         executor = "sge"
         cpus = 16
         memory = "5GB"
@@ -69,7 +71,8 @@ profiles {
         penv = 'openmp16'
       }
       withName: filter_fasta {
-        beforeScript = "module purge; module load bioawk/1.0"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "bioawk/1.0"
         executor = "sge"
         cpus = 1
         memory = "20GB"
@@ -77,7 +80,8 @@ profiles {
         queue = 'monointeldeb128'
       }
       withName: index_fasta {
-        beforeScript = "module purge; module load Bowtie2/2.3.4.1; module load sambamba/0.6.7; module load samblaster/0.6.7"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "Bowtie2/2.3.4.1:sambamba/0.6.7:samblaster/0.1.24"
         executor = "sge"
         cpus = 1
         memory = "30GB"
@@ -85,7 +89,8 @@ profiles {
         queue = 'monointeldeb128'
       }
       withName: mapping_fastq {
-        beforeScript = "module purge; module load Bowtie2/2.3.4.1"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "Bowtie2/2.3.4.1:sambamba/0.6.7:samblaster/0.1.24"
         executor = "sge"
         cpus = 16
         memory = "30GB"
@@ -94,7 +99,8 @@ profiles {
         penv = 'openmp16'
       }
       withName: merge_bam {
-        beforeScript = "module purge; module load sambamba/0.6.7"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "sambamba/0.6.7"
         executor = "sge"
         cpus = 16
         memory = "30GB"
@@ -103,7 +109,8 @@ profiles {
         penv = 'openmp16'
       }
       withName: sort_bam {
-        beforeScript = "module purge; module load sambamba/0.6.7"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "sambamba/0.6.7"
         executor = "sge"
         cpus = 16
         memory = "30GB"
@@ -112,7 +119,8 @@ profiles {
         penv = 'openmp16'
       }
       withName: index_bam {
-        beforeScript = "module purge; module load sambamba/0.6.7"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "sambamba/0.6.7"
         executor = "sge"
         cpus = 16
         memory = "30GB"
@@ -121,7 +129,8 @@ profiles {
         penv = 'openmp16'
       }
       withName: index2_fasta {
-        beforeScript = "module purge; module load GATK/4.0.8.1"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "GATK/4.0.10.1"
         executor = "sge"
         cpus = 1
         memory = "20GB"
@@ -129,7 +138,8 @@ profiles {
         queue = 'monointeldeb128'
       }
       withName: index3_fasta {
-        beforeScript = "module purge; module load SAMtools/1.7"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "SAMtools/1.7"
         executor = "sge"
         cpus = 1
         memory = "20GB"
@@ -137,7 +147,8 @@ profiles {
         queue = 'monointeldeb128'
       }
       withName: samtools_SNP_tumor {
-        beforeScript = "module purge; module load BCFtools/1.7"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "BCFtools/1.7"
         executor = "sge"
         cpus = 1
         memory = "20GB"
@@ -145,7 +156,8 @@ profiles {
         queue = 'monointeldeb128'
       }
       withName: samtools_SNP_norm {
-        beforeScript = "module purge; module load BCFtools/1.7"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "BCFtools/1.7"
         executor = "sge"
         cpus = 1
         memory = "20GB"
@@ -153,7 +165,8 @@ profiles {
         queue = 'monointeldeb128'
       }
       withName: vcf_to_csv_tumor {
-        beforeScript = "module purge; module load GATK/4.0.8.1"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "GATK/4.0.10.1"
         executor = "sge"
         cpus = 1
         memory = "20GB"
@@ -161,7 +174,8 @@ profiles {
         queue = 'monointeldeb128'
       }
       withName: vcf_to_csv_norm {
-        beforeScript = "module purge; module load GATK/4.0.8.1"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "GATK/4.0.10.1"
         executor = "sge"
         cpus = 1
         memory = "20GB"