SNP_calling.config: add docker configs

src/SNP_calling.config

@@ -3,23 +3,41 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $adaptor_removal {
+      withName: adaptor_removal {
         container = "cutadapt:1.14"
       }
-      $trimming {
+      withName: trimming {
         container = "urqt:d62c1f8"
       }
-      $index_fasta {
+      withName: index_fasta {
         container = "bwa:0.7.17"
       }
-      $mapping_fastq {
+      withName: mapping_fastq {
         container = "bwa:0.7.17"
       }
+      withName: dedup_sam {
+        container = "samblaster:0.1.24"
+      }
+      withName: sort_bam {
+        container = "sambamba:0.6.7"
+      }
+      withName: index_bam {
+        container = "sambamba:0.6.7"
+      }
+      withName: index2_fasta {
+        container = "gatk:4.0.8.1"
+      }
+      withName: index3_fasta {
+        container = "samtools:1.7"
+      }
+      withName: HaplotypeCaller {
+        container = "gatk:4.0.8.1"
+      }
     }
   }
   sge {
     process{
-      $adaptor_removal {
+      withName: adaptor_removal {
         beforeScript = "module purge; module load cutadapt/1.14"
         executor = "sge"
         cpus = 1
@@ -30,7 +48,7 @@ profiles {
         queue = 'h6-E5-2667v4deb128'
         penv = 'openmp8'
       }
-      $trimming {
+      withName: trimming {
         beforeScript = "module purge; module load UrQt/d62c1f8"
         executor = "sge"
         cpus = 4
@@ -41,7 +59,7 @@ profiles {
         queue = 'h6-E5-2667v4deb128'
         penv = 'openmp8'
       }
-      $index_fasta {
+      withName: index_fasta {
         beforeScript = "module purge; module load BWA/0.7.17"
         executor = "sge"
         cpus = 1
@@ -52,7 +70,7 @@ profiles {
         queue = 'h6-E5-2667v4deb128'
         penv = 'openmp8'
       }
-      $mapping_fastq {
+      withName: mapping_fastq {
         beforeScript = "module purge; module load BWA/0.7.17"
         executor = "sge"
         cpus = 4
@@ -63,6 +81,9 @@ profiles {
         queue = 'h6-E5-2667v4deb128'
         penv = 'openmp8'
       }
+      withName: dedup_sam {
+        beforeScript = "module purge; module load samblaster/0.1.24"
+      }
     }
   }
 }