kallisto: add in2p3 config

src/nf_modules/kallisto/indexing.config

@@ -42,11 +42,9 @@ profiles {
         stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
-        cpus = 4
-        memory = "8GB"
+        cpus = 1
+        memory = "10GB"
         time = "24h"
-        queue = 'mc_huge'
-        penv = 'multicores'
       }
     }
   }

src/nf_modules/kallisto/mapping_paired.config

@@ -33,6 +33,21 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    process{
+      withName: mapping_fastq {
+        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/kallisto/0.44.0/:/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/kallisto/mapping_single.config

@@ -33,6 +33,21 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    process{
+      withName: mapping_fastq {
+        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/kallisto/0.44.0/:/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"
+      }
+    }
+  }
 }