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federicacitarrella · Jan 28, 2022 · 54b4cbb · 54b4cbb
1 parent 6fed10b
commit 54b4cbb
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Showing 2 changed files with 84 additions and 81 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -2,7 +2,7 @@ manifest {
     mainScript = 'pipeline.nf'
 }
 
-params { 
+params {
   help = false
   dnabam = false
   single_end = false
@@ -29,40 +29,48 @@ params {
   dnareads_tumor = ""
   dnareads_normal = ""
 
-  envPath_ericscript = "/opt/conda/envs/ericscript/bin"
-  envPath_arriba = "/opt/conda/envs/arriba/"
-  envPath_fusioncatcher = "/opt/conda/envs/fusioncatcher/bin"
-  envPath_integrate = "/opt/conda/envs/integrate/bin"
-  envPath_genefuse = "/opt/conda/envs/genefuse/bin"
+  envPath_ericscript = "/homes/gbontempo/.conda/envs/ericscript/bin"
+  envPath_arriba = "/homes/gbontempo/.conda/envs/arriba/"
+  envPath_fusioncatcher = "/homes/gbontempo/.conda/envs/fusioncatcher/bin"
+  envPath_integrate = "/homes/gbontempo/.conda/envs/integrate/bin"
+  envPath_genefuse = "/homes/gbontempo/.conda/envs/genefuse/bin"
 
   nthreads = 8
-  max_cpus = 16  
-} 
+  max_cpus = 16
+}
 
 process {
+    executor = "slurm"
+    memory = '20GB'
+    queue= 'prod'
+    cpus= 3
     container = 'federicacitarrella/pipeline:latest'
-    publishDir = [path: params.outdir, mode: 'copy', overwrite: 'true']
-} 
+}
+
+executor {
+    memory = '20GB'
+
+}
 
 profiles {
     local {
-      params.feelnc_opts = "--monoex=1 --size=50 --minfrac_over=1.0 " 
+      params.feelnc_opts = "--monoex=1 --size=50 --minfrac_over=1.0 "
     }
     docker {
-      params.feelnc_opts = "--monoex=1 --size=50 --minfrac_over=1.0 " 
+      params.feelnc_opts = "--monoex=1 --size=50 --minfrac_over=1.0 "
       docker.enabled = true
       docker.fixOwnership = true
     }
     test_docker{
       params.rnareads  = "$baseDir/tutorial/reads_{1,2}.fq.gz"
       params.dnareads_tumor  = "$baseDir/tutorial/reads_{3,4}.fq.gz"
-      params.feelnc_opts = "--monoex=1 --size=50 --minfrac_over=1.0 " 
+      params.feelnc_opts = "--monoex=1 --size=50 --minfrac_over=1.0 "
       docker.enabled = true
       docker.fixOwnership = true
     }
     test_local{
       params.rnareads  = "$baseDir/tutorial/reads_{1,2}.fq.gz"
       params.dnareads_tumor  = "$baseDir/tutorial/reads_{3,4}.fq.gz"
-      params.feelnc_opts = "--monoex=1 --size=50 --minfrac_over=1.0 " 
+      params.feelnc_opts = "--monoex=1 --size=50 --minfrac_over=1.0 "
     }
 }