From c8de9be7014ee85359caddc04aefd725974d5d6b Mon Sep 17 00:00:00 2001
From: Daniel Lundin <erik.rikard.daniel@gmail.com>
Date: Tue, 31 Mar 2020 15:17:24 +0200
Subject: [PATCH] Adding UPPMAX specific config for ampliseq

---
 conf/pipeline/ampliseq/uppmax.config | 15 +++++++++++++++
 docs/pipeline/ampliseq/uppmax.md     | 17 +++++++++++++++++
 pipeline/ampliseq.config             |  6 +++++-
 3 files changed, 37 insertions(+), 1 deletion(-)
 create mode 100644 conf/pipeline/ampliseq/uppmax.config
 create mode 100644 docs/pipeline/ampliseq/uppmax.md

diff --git a/conf/pipeline/ampliseq/uppmax.config b/conf/pipeline/ampliseq/uppmax.config
new file mode 100644
index 0000000..36a1c3b
--- /dev/null
+++ b/conf/pipeline/ampliseq/uppmax.config
@@ -0,0 +1,15 @@
+// Profile config names for nf-core/configs
+
+params {
+  // Specific nf-core/configs params
+  config_profile_contact = 'Daniel Lundin (daniel.lundin@lnu.se)'
+  config_profile_description = 'nf-core/ampliseq UPPMAX profile provided by nf-core/configs'
+}
+
+withName: make_SILVA_132_16S_classifier {
+  clusterOptions = { "-A $params.project -C fat -p node -N 1 ${params.clusterOptions ?: ''}" }
+}
+
+withName: classifier {
+  clusterOptions = { "-A $params.project -C fat -p node -N 1 ${params.clusterOptions ?: ''}" }
+}
diff --git a/docs/pipeline/ampliseq/uppmax.md b/docs/pipeline/ampliseq/uppmax.md
new file mode 100644
index 0000000..7061bdc
--- /dev/null
+++ b/docs/pipeline/ampliseq/uppmax.md
@@ -0,0 +1,17 @@
+# nf-core/configs: uppmax ampliseq specific configuration
+
+Extra specific configuration for the ampliseq pipeline.
+
+## Usage
+
+To use, run the pipeline with `-profile uppmax`.
+
+This will download and launch the ampliseq specific [`uppmax.config`](../../../conf/pipeline/ampliseq/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX cluster.
+
+Example: `nextflow run nf-core/ampliseq -profile uppmax`
+
+## ampliseq specific configurations for uppmax
+
+Specific configurations for UPPMAX has been made for ampliseq.
+
+* Makes sure that a fat node is allocated for training and applying a Bayesian classifier.
diff --git a/pipeline/ampliseq.config b/pipeline/ampliseq.config
index 6009d68..7b36722 100644
--- a/pipeline/ampliseq.config
+++ b/pipeline/ampliseq.config
@@ -10,4 +10,8 @@
 
 profiles {
   binac { includeConfig "${params.custom_config_base}/conf/pipeline/ampliseq/binac.config" }
-}
\ No newline at end of file
+}
+
+profiles {
+  uppmax { includeConfig "${params.custom_config_base}/conf/pipeline/ampliseq/uppmax.config" }
+}