Custom config for nf-core eager on Crick's data and cluster

conf/pipeline/eager/custom.config

@@ -0,0 +1,57 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow custom config file for running nf-core eager on data generated at the Francis Crick Institute
+ *  contact: Alexandre Gilardet alexandre.gilardet@crick.ac.uk
+ * -------------------------------------------------
+ * nextflow run nf-core/eager -profile <profile>,crick -c custom.config 
+ * (where <profile> is screening or production for low or high-coverage data 
+ * respectively, or external for very high coverage)
+ */
+
+profiles {
+  screening {
+    process {
+      withName:bwa {
+        cpus = 12
+        memory = '15 GB'
+        time = '6h'
+      }
+    }
+  }
+  production {
+    process {
+      withName:adapter_removal {
+        time = '3d'
+      }
+      withName:fastp {
+        time = '8h'
+      }
+      withName:bwa {
+        cpus = 8
+        memory = '56 GB'
+        time = '3d'
+      }
+      withName:samtools_filter {
+        time = '3d'
+      }
+      withName:dedup {
+        cpus = 6
+        memory = '20 GB'
+        time = '3d'
+      }
+      withName:damageprofiler {
+        memory = '64 GB'
+        time = '3d'
+        errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' }
+      }
+    }  
+  }
+  external {
+    process {
+      withName:samtools_filter {
+        cpus = 12
+        memory = '72 GB'
+      }
+    }
+  }
+}