From d24a296a016e437ec62babc81bd2004f35629be5 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Wed, 11 Mar 2020 14:02:01 +0100
Subject: [PATCH] add munin/rnafusion specific config

---
 conf/pipeline/rnafusion/munin.config | 64 ++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100644 conf/pipeline/rnafusion/munin.config

diff --git a/conf/pipeline/rnafusion/munin.config b/conf/pipeline/rnafusion/munin.config
new file mode 100644
index 0000000..d44a1f3
--- /dev/null
+++ b/conf/pipeline/rnafusion/munin.config
@@ -0,0 +1,64 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for Munin Singularity
+ * -------------------------------------------------
+ */
+
+params {
+  max_cpus = 24
+  max_memory = 256.GB
+  max_time = 72.h
+  container_version = '1.1.0'
+
+  // Tool versions
+  arriba_version = '1.1.0'
+  ericscript_version = '0.5.5'
+  fusioncatcher_version = '1.20'
+  fusion_inspector_version = '1.3.1-star2.7.0f'
+  pizzly_version = '0.37.3'
+  squid_version = '1.5-star2.7.0f'
+  star_fusion_version = '1.6.0'
+
+  // Paths
+  reference_base = '/data1/references/rnafusion'
+  containerPath = "file:///data1/containers/rnafusion_containers_v${container_version}"
+  containerPathCommon = "file:///data1/containers/rnafusion_common"
+  
+  // References
+  fasta = "${params.reference_base}/1.1.0/Homo_sapiens.GRCh38_r97.all.fa"
+  gtf = "${params.reference_base}/1.1.0/Homo_sapiens.GRCh38_r97.gtf"
+  transcript = "${params.reference_base}/1.1.0/Homo_sapiens.GRCh38_r97.cdna.all.fa.gz"
+  databases = "${params.reference_base}/1.1.0/databases"
+  
+  star_index = "${params.reference_base}/1.1.0/star_index/star"
+  arriba_ref = "${params.reference_base}/arriba_ref"
+  fusioncatcher_ref = "${params.reference_base}/fusioncatcher_ref/human_v98"
+  star_fusion_ref = "${params.reference_base}/star_fusion/1.6.0/ensembl/ctat_genome_lib_build_dir"
+  ericscript_ref = "${params.reference_base}/ericscript_ref/ericscript_db_homosapiens_ensembl84" 
+}
+
+process {
+  container = "${params.containerPath}/rnafusion_1.1.0.img"
+
+  withName: "arriba|arriba_visualization" {
+    container = "${params.containerPath}/rnafusion_arriba_v${params.arriba_version}.img"
+  }
+  withName: "star_fusion|download_star_fusion" {
+    container = "${params.containerPath}/rnafusion_star-fusion_v${params.star_fusion_version}.img"
+  }
+  withName:fusioncatcher {
+    container = "${params.containerPath}/rnafusion_fusioncatcher_v${params.fusioncatcher_version}.img"
+  }
+  withName:fusion_inspector {
+    container = "${params.containerPath}/rnafusion_fusion-inspector_v${params.fusion_inspector_version}.img"
+  }
+  withName:ericscript {
+    container = "${params.containerPathCommon}/rnafusion_ericscript_v${params.ericscript_version}.img"
+  }
+  withName:pizzly {
+    container = "${params.containerPathCommon}/rnafusion_pizzly_v${params.pizzly_version}.img"
+  }
+  withName:squid {
+    container = "${params.containerPath}/rnafusion_squid_v${params.squid_version}.img"
+  }
+}
\ No newline at end of file