From 44696c604057e9b56ba661f37d031e69231fff89 Mon Sep 17 00:00:00 2001
From: alexandregilardet <63741852+alexandregilardet@users.noreply.github.com>
Date: Tue, 15 Mar 2022 14:13:58 +0000
Subject: [PATCH] Custom config for nf-core eager on Crick's data and cluster

---
 conf/pipeline/eager/custom.config | 57 +++++++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 conf/pipeline/eager/custom.config

diff --git a/conf/pipeline/eager/custom.config b/conf/pipeline/eager/custom.config
new file mode 100644
index 0000000..3543b7e
--- /dev/null
+++ b/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'
+      }
+    }
+  }
+}