Merge pull request #150 from MaxUlysse/Munin

update rnafusion munin specific config

conf/pipeline/rnafusion/munin.config

@@ -4,57 +4,7 @@ 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"
-  }
+  genomes_base = '/data1/references/rnafusion/dev/'
 }

docs/pipeline/rnafusion/munin.md

@@ -15,5 +15,4 @@ Example: `nextflow run nf-core/rnafusion -profile munin`
 Specific configurations for `MUNIN` has been made for rnafusion.
 
 * `cpus`, `memory` and `time` max requirements.
-* Paths to specific containers
 * Paths to specific references and indexes

pipeline/rnafusion.config

@@ -0,0 +1,13 @@
+/*
+ * -------------------------------------------------
+ *  nfcore/rnafusion custom profile Nextflow config file
+ * -------------------------------------------------
+ * Config options for custom environments.
+ * Cluster-specific config options should be saved
+ * in the conf/pipeline/rnafusion folder and imported
+ * under a profile name here.
+ */
+
+profiles {
+  munin { includeConfig "${params.custom_config_base}/conf/pipeline/rnafusion/munin.config" }
+}