From cd1d0b5f8f52ced05548cbd3b6dddd680cf890e7 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Wed, 20 Nov 2019 10:10:05 +0100
Subject: [PATCH] Add specific sarek config base, munin specific sarek config
 and docs

rename file

improve configs

remove unnecessary params
---
 conf/munin.config                | 26 +++++++++++---------------
 conf/pipeline/sarek/munin.config | 26 ++++++++++++++++++++++++++
 docs/pipeline/sarek/munin.md     | 21 +++++++++++++++++++++
 pipeline/sarek.config            | 13 +++++++++++++
 4 files changed, 71 insertions(+), 15 deletions(-)
 create mode 100644 conf/pipeline/sarek/munin.config
 create mode 100644 docs/pipeline/sarek/munin.md
 create mode 100644 pipeline/sarek.config

diff --git a/conf/munin.config b/conf/munin.config
index f53def4..e642ec6 100644
--- a/conf/munin.config
+++ b/conf/munin.config
@@ -1,8 +1,13 @@
-//Profile config names for nf-core/configs
+// Profile config names for nf-core/configs
+
 params {
-  config_profile_description = 'MUNIN profile provided by nf-core/configs.'
+  // Specific nf-core/configs params
   config_profile_contact = 'Szilveszter Juhos (@szilva)'
-  config_profile_url = ''
+  config_profile_description = 'MUNIN profile provided by nf-core/configs.'
+  config_profile_url = 'https://ki.se/forskning/barntumorbanken'
+
+  // Local AWS iGenomes reference file paths on munin
+  igenomes_base = '/data1/references/igenomes/'
 }
 
 process {
@@ -10,9 +15,10 @@ process {
   maxForks = 46
 }
 
-// To use singularity, use nextflow run -profile munin,singularity
+// To use singularity, use nextflow run -profile munin
 singularity {
   enabled = true
+  cacheDir = '/data1/containers/'
 }
 
 // To use docker, use nextflow run -profile munin,docker
@@ -20,14 +26,4 @@ docker {
   enabled = false
   mountFlags = 'z'
   fixOwnership = true
-}
-
-params {
-  // general params
-  max_memory = 752.GB
-  max_cpus = 46
-  max_time = 72.h
-
-  // Local AWS iGenomes reference file paths on munin
-  igenomes_base = '/data1/references/igenomes/'
-}
+}
\ No newline at end of file
diff --git a/conf/pipeline/sarek/munin.config b/conf/pipeline/sarek/munin.config
new file mode 100644
index 0000000..8655a2f
--- /dev/null
+++ b/conf/pipeline/sarek/munin.config
@@ -0,0 +1,26 @@
+// Profile config names for nf-core/configs
+
+params {
+  // Specific nf-core/configs params
+  config_profile_contact = 'Maxime Garcia (@MaxUlysse)'
+  config_profile_description = 'nf-core/sarek MUNIN profile provided by nf-core/configs'
+  config_profile_url = 'https://ki.se/forskning/barntumorbanken'
+
+  // Specific nf-core/sarek configs params
+  max_memory = 752.GB
+  max_cpus = 46
+  max_time = 72.h
+
+  // Specific nf-core/sarek params
+  annotation_cache = true
+  pon = '/data1/PON/vcfs/BTB.PON.vcf.gz'
+  pon_index = '/data1/PON/vcfs/BTB.PON.vcf.gz.tbi'
+  snpEff_cache = '/data1/cache/snpEff/'
+  vep_cache = '/data1/cache/VEP/'
+}
+
+// Specific nf-core/sarek configuration
+withLabel:sentieon {
+  module = {params.sentieon ? 'sentieon/201808.05' : ''}
+  container = {params.sentieon ? '' : 'nfcore/sarek:dev'}
+}
diff --git a/docs/pipeline/sarek/munin.md b/docs/pipeline/sarek/munin.md
new file mode 100644
index 0000000..24c4404
--- /dev/null
+++ b/docs/pipeline/sarek/munin.md
@@ -0,0 +1,21 @@
+# nf-core/configs: MUNIN sarek specific configuration
+
+Extra specific configuration for sarek pipeline
+
+## Usage
+
+To use, run the pipeline with `-profile munin`.
+
+This will download and launch the [`munin.config`](../conf/pipeline/sarek/munin.config) which has been pre-configured with a setup suitable for the MUNIN cluster.
+
+Example: `nextflow run nf-core/sarek -profile munin`
+
+## Sarek specific configurations for Munin
+
+Specific configurations for Munin has been made for sarek.
+
+* Path to `snpEff_cache`: `/data1/cache/snpEff/`
+* Path to `vep_cache`: `/data1/cache/VEP/`
+* Path to `pon`: `/data1/PON/vcfs/BTB.PON.vcf.gz`
+* Path to `pon_index`: `/data1/PON/vcfs/BTB.PON.vcf.gz.tbi`
+* Load module `Sentieon` for Process with `sentieon` labels 
\ No newline at end of file
diff --git a/pipeline/sarek.config b/pipeline/sarek.config
new file mode 100644
index 0000000..6935794
--- /dev/null
+++ b/pipeline/sarek.config
@@ -0,0 +1,13 @@
+/*
+ * -------------------------------------------------
+ *  nfcore/sarek custom profile Nextflow config file
+ * -------------------------------------------------
+ * Config options for all custom environments.
+ * Cluster-specific config options should be saved
+ * in the conf/pipeline/sarek folder and imported
+ * under a profile name here.
+ */
+
+profiles {
+  munin { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/munin.config" }
+}
\ No newline at end of file