From c583aa0233bf5fd5769db4db3046fd66a5fb99e8 Mon Sep 17 00:00:00 2001
From: Martin Proks <mproksik@gmail.com>
Date: Mon, 5 Aug 2019 11:19:06 +0200
Subject: [PATCH] Added kraken config (#15)

* Added kraken template
* docs: updated some info
* fix: updated igenomes_base path
---
 conf/kraken.config | 24 ++++++++++++++++++++++++
 docs/kraken.md     | 10 ++++++++++
 2 files changed, 34 insertions(+)
 create mode 100644 conf/kraken.config
 create mode 100644 docs/kraken.md

diff --git a/conf/kraken.config b/conf/kraken.config
new file mode 100644
index 0000000..59417e9
--- /dev/null
+++ b/conf/kraken.config
@@ -0,0 +1,24 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_name = 'KRAKEN'
+  config_profile_description = 'Jenkins cluster provided by nf-core/configs.'
+  config_profile_contact = 'Maxime Garcia or Johannes Alneberg'
+  config_profile_url = 'kraken.dyn.scilifelab.se'
+}
+
+process {
+  executor = 'local'
+}
+
+docker {
+  enabled = true
+  mountFlags = 'z'
+  fixOwnership = true
+}
+
+params {
+  max_memory = 60.GB
+  max_cpus = 16
+  max_time = 72.h
+  igenomes_base = '/share/igenomes/'
+}
diff --git a/docs/kraken.md b/docs/kraken.md
new file mode 100644
index 0000000..9426087
--- /dev/null
+++ b/docs/kraken.md
@@ -0,0 +1,10 @@
+# nf-core/configs: KRAKEN Configuration
+
+This profile can be **only** combined with `jenkins.config`. It is used for
+testing pipeline with real data on **in-house** cluster located at SciLifeLab.
+
+To use, run the pipeline with `-profile kraken`. This will download and launch
+the [`kraken.config`](../conf/kraken.config) which has been pre-configured to
+test the pipeline using `docker` by default.
+
+Example: `nextflow run -profile kraken,jenkins`