Added bianca.config

Author: viklund

config/bianca.config

@@ -0,0 +1,46 @@
+process {
+    $index_bamfile {
+        module = ['bioinfo-tools', 'samtools/1.3']
+    }
+
+    $manta {
+        maxRetries = 3
+        cpus = 16
+        module = ['bioinfo-tools', 'manta/1.0.3']
+    }
+
+    $create_fastq {
+        module = ['bioinfo-tools', 'samtools/1.3']
+    }
+
+    $fermikit {
+        maxRetries = 3
+        cpus = 16
+        module = ['bioinfo-tools', 'samtools/1.3', 'fermikit/r178', "vcftools/0.1.14", "tabix/0.2.6"]
+    }
+
+    $artifact_mask_vcfs {
+        module = ['bioinfo-tools', 'BEDTools/2.26.0']
+    }
+
+    $swegen_mask_vcfs {
+        module = ['bioinfo-tools', 'BEDTools/2.26.0']
+    }
+
+    $intersect_files {
+        module = ['bioinfo-tools', 'BEDTools/2.26.0']
+    }
+
+    $normalize_vcf {
+        module = ['bioinfo-tools', 'vt/0.5772']
+    }
+
+    $variant_effect_predictor {
+        cpus = 4
+        module = ['bioinfo-tools', 'vep/84']
+    }
+
+    $snpEff {
+        module = ['bioinfo-tools', 'snpEff/4.2', 'vt/0.5772']
+    }
+}

nextflow.config

@@ -36,6 +36,11 @@ profiles {
         includeConfig 'config/milou.config'
     }
 
+    bianca {
+        includeConfig 'config/standard.config'
+        includeConfig 'config/bianca.config'
+    }
+
     devel {
         includeConfig 'config/devcore.config'
         includeConfig 'config/milou.config'