samtools: add in2p3 config

src/nf_modules/samtools/filter_bams.config

@@ -33,4 +33,19 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    process{
+      withName: filter_bam {
+        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$PATH"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        memory = "10GB"
+        time = "24h"
+      }
+    }
+  }
 }

src/nf_modules/samtools/index_bams.config

@@ -32,4 +32,19 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    process{
+      withName: index_bam {
+        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$PATH"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        memory = "10GB"
+        time = "24h"
+      }
+    }
+  }
 }

src/nf_modules/samtools/sort_bams.config

@@ -33,4 +33,19 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    process{
+      withName: sort_bam {
+        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$PATH"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        memory = "10GB"
+        time = "24h"
+      }
+    }
+  }
 }

src/nf_modules/samtools/split_bams.config

@@ -32,4 +32,19 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    process{
+      withName: split_bam {
+        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$PATH"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        memory = "10GB"
+        time = "24h"
+      }
+    }
+  }
 }