nf modules: add ccin2p3 profile

src/nf_modules/samtools/split_bams.config

@@ -48,4 +48,21 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }

src/nf_modules/sratoolkit/fastqdump.config

@@ -48,4 +48,21 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }

src/nf_modules/urqt/trimming_paired.config

@@ -49,5 +49,22 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }
 

src/nf_modules/urqt/trimming_single.config

@@ -49,5 +49,22 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }