From 5a67eba04cf0d8850dd2a5b805e3a830cafa9de9 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Fri, 3 Jun 2022 12:41:08 +0200
Subject: [PATCH] Add MAG @ EVA profile

---
 README.md                                      |  2 ++
 conf/pipeline/mag/eva.config                   | 14 ++++++++++++++
 docs/pipeline/eager/{mpcdf.config => mpcdf.md} |  0
 docs/pipeline/mag/eva.md                       | 15 +++++++++++++++
 pipeline/mag.config                            | 13 +++++++++++++
 5 files changed, 44 insertions(+)
 create mode 100644 conf/pipeline/mag/eva.config
 rename docs/pipeline/eager/{mpcdf.config => mpcdf.md} (100%)
 create mode 100644 docs/pipeline/mag/eva.md
 create mode 100644 pipeline/mag.config

diff --git a/README.md b/README.md
index 43b8c71..7224aab 100644
--- a/README.md
+++ b/README.md
@@ -192,6 +192,8 @@ Currently documentation is available for the following pipelines within specific
   - [UPPMAX](docs/pipeline/ampliseq/uppmax.md)
 - eager
   - [EVA](docs/pipeline/eager/eva.md)
+- mag
+  - [EVA](docs/pipeline/mag/eva.md)
 - rnafusion
   - [MUNIN](docs/pipeline/rnafusion/munin.md)
 - rnavar
diff --git a/conf/pipeline/mag/eva.config b/conf/pipeline/mag/eva.config
new file mode 100644
index 0000000..81d8d0c
--- /dev/null
+++ b/conf/pipeline/mag/eva.config
@@ -0,0 +1,14 @@
+params {
+  // Specific nf-core/configs params
+  config_profile_contact = 'James Fellows Yates (@jfy133)'
+  config_profile_description = 'nf-core/mag EVA profile provided by nf-core/configs'
+}
+
+process {
+
+    withName: FASTQC {
+    clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
+    }
+
+}
diff --git a/docs/pipeline/eager/mpcdf.config b/docs/pipeline/eager/mpcdf.md
similarity index 100%
rename from docs/pipeline/eager/mpcdf.config
rename to docs/pipeline/eager/mpcdf.md
diff --git a/docs/pipeline/mag/eva.md b/docs/pipeline/mag/eva.md
new file mode 100644
index 0000000..7ba5eec
--- /dev/null
+++ b/docs/pipeline/mag/eva.md
@@ -0,0 +1,15 @@
+# nf-core/configs: eva mag specific configuration
+
+Extra specific configuration for mag pipeline
+
+## Usage
+
+To use, run the pipeline with `-profile eva`.
+
+This will download and launch the eager specific [`eva.config`](../../../conf/pipeline/mag/eva.config) which has been pre-configured with a setup suitable for the MPI-EVA cluster.
+
+Example: `nextflow run nf-core/eager -profile eva`
+
+## mag specific configurations for eva
+
+Specific configurations for eva has been made for mag, primarily adjusting SGE memory requirements of Java tools (e.g. FastQC).
diff --git a/pipeline/mag.config b/pipeline/mag.config
new file mode 100644
index 0000000..f45a59a
--- /dev/null
+++ b/pipeline/mag.config
@@ -0,0 +1,13 @@
+/*
+ * -------------------------------------------------
+ *  nfcore/eager custom profile Nextflow config file
+ * -------------------------------------------------
+ * Config options for custom environments.
+ * Cluster-specific config options should be saved
+ * in the conf/pipeline/mag folder and imported
+ * under a profile name here.
+ */
+
+profiles {
+  eva { includeConfig "${params.custom_config_base}/conf/pipeline/mag/eva.config" }
+}