From 731372dac24d8b6cf5cb38e3016e4eec260e9db7 Mon Sep 17 00:00:00 2001
From: jfy133 <jfy133@gmail.com>
Date: Thu, 5 Dec 2019 17:01:10 +0100
Subject: [PATCH 1/2] Added SHH specific EAGER configuration

---
 conf/pipeline/eager/shh.config | 17 +++++++++++++++++
 docs/pipeline/eager/shh.md     | 17 +++++++++++++++++
 pipeline/eager.config          | 13 +++++++++++++
 3 files changed, 47 insertions(+)
 create mode 100644 conf/pipeline/eager/shh.config
 create mode 100644 docs/pipeline/eager/shh.md
 create mode 100644 pipeline/eager.config

diff --git a/conf/pipeline/eager/shh.config b/conf/pipeline/eager/shh.config
new file mode 100644
index 0000000..3dd95ed
--- /dev/null
+++ b/conf/pipeline/eager/shh.config
@@ -0,0 +1,17 @@
+// Profile config names for nf-core/configs
+
+params {
+  // Specific nf-core/configs params
+  config_profile_contact = 'James Fellows Yates (@jfy133)'
+  config_profile_description = 'nf-core/eager SHH profile provided by nf-core/configs'
+}
+
+// Specific nf-core/eager process configuration
+process {
+  withName: malt {
+    memory = { check_max( 756.GB * task.attempt, 'memory' ) }
+    cpus = { check_max(64 * task.attempt, 'cpus') }
+    time = 1440.h
+    queue = { task.memory > 756.GB ? 'supercruncher': 'long' }
+  }
+}
diff --git a/docs/pipeline/eager/shh.md b/docs/pipeline/eager/shh.md
new file mode 100644
index 0000000..8d6f7fe
--- /dev/null
+++ b/docs/pipeline/eager/shh.md
@@ -0,0 +1,17 @@
+# nf-core/configs: shh eager specific configuration
+
+Extra specific configuration for eager pipeline
+
+## Usage
+
+To use, run the pipeline with `-profile shh`.
+
+This will download and launch the eager specific [`shh.config`](../conf/pipeline/eager/shh.config) which has been pre-configured with a setup suitable for the shh cluster.
+
+Example: `nextflow run nf-core/eager -profile shh`
+
+## eager specific configurations for shh
+
+Specific configurations for shh has been made for eager.
+
+* Running with the MALT module turned on, will by default be sent either to long or supercruncher queues with a minimum of 756GB and 64 cores.
\ No newline at end of file
diff --git a/pipeline/eager.config b/pipeline/eager.config
new file mode 100644
index 0000000..36f7cae
--- /dev/null
+++ b/pipeline/eager.config
@@ -0,0 +1,13 @@
+/*
+ * -------------------------------------------------
+ *  nfcore/eager custom profile Nextflow config file
+ * -------------------------------------------------
+ * Config options for custom environments.
+ * Cluster-specific config options should be saved
+ * in the conf/pipeline/eager folder and imported
+ * under a profile name here.
+ */
+
+profiles {
+  shh { includeConfig "${params.custom_config_base}/conf/pipeline/eager/shh.config" }
+}
\ No newline at end of file

From 1650080b6e45fa4f532458cd07bd8cc8baaaf874 Mon Sep 17 00:00:00 2001
From: jfy133 <jfy133@gmail.com>
Date: Thu, 5 Dec 2019 17:03:07 +0100
Subject: [PATCH 2/2] Linting

---
 docs/pipeline/eager/shh.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/pipeline/eager/shh.md b/docs/pipeline/eager/shh.md
index 8d6f7fe..8921a54 100644
--- a/docs/pipeline/eager/shh.md
+++ b/docs/pipeline/eager/shh.md
@@ -14,4 +14,4 @@ Example: `nextflow run nf-core/eager -profile shh`
 
 Specific configurations for shh has been made for eager.
 
-* Running with the MALT module turned on, will by default be sent either to long or supercruncher queues with a minimum of 756GB and 64 cores.
\ No newline at end of file
+* Running with the MALT module turned on, will by default be sent either to long or supercruncher queues with a minimum of 756GB and 64 cores.