output published correctly

Author: Bontempogianpaolo1

nextflow.config

@@ -29,24 +29,27 @@ 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
 }
 
 process {
+    executor = "slurm"
+    memory = '20GB'
+    queue= 'prod'
+    cpus= 3
     container = 'federicacitarrella/pipeline:latest'
-    publishDir = [path: params.outdir, mode: 'copy', overwrite: 'true']
 }
 
 executor {
-    name   = 'local'
-    memory = '9GB'
+    memory = '20GB'
+
 }
 
 profiles {

pipeline.nf

@@ -241,8 +241,7 @@ process ericscript{
     tuple pair_id, file(rna_reads), file(ericscript_db) from rna_reads_ericscript.combine(ch2_ericscript.mix(ch3_ericscript))
 
     output:
-    file "output/${pair_id}" into ericscript_fusions
-
+    file "output/${pair_id}/*" into ericscript_fusions
     when: params.ericscript || !(params.arriba || params.ericscript || params.fusioncatcher || params.genefuse || params.integrate)
 
     script:
@@ -273,7 +272,7 @@ process arriba_downloader{
     val x from ch1_arriba
 
     output:
-    file "files" into ch3_arriba
+    file "files/**" into ch3_arriba
 
     when: params.arriba || !(params.arriba || params.ericscript || params.fusioncatcher || params.genefuse || params.integrate)
 
@@ -333,7 +332,7 @@ process fusioncatcher_downloader{
     val x from ch1_fusioncatcher
 
     output:
-    file "files" into ch3_fusioncatcher
+    file "files/*" into ch3_fusioncatcher
 
     when: params.fusioncatcher || !(params.arriba || params.ericscript || params.fusioncatcher || params.genefuse || params.integrate)
 
@@ -363,7 +362,7 @@ process fusioncatcher{
     tuple pair_id, file(rna_reads), file(fusioncatcher_db) from rna_reads_fusioncatcher.combine(ch2_fusioncatcher.mix(ch3_fusioncatcher))
 
     output:
-    file "output/${pair_id}" optional true into fusioncatcher_fusions
+    file "output/${pair_id}/*" optional true into fusioncatcher_fusions
 
     when: params.fusioncatcher || !(params.arriba || params.ericscript || params.fusioncatcher || params.genefuse || params.integrate)