small fixies

Author: Bontempogianpaolo1

pipeline.nf

@@ -147,9 +147,6 @@ process referenceGenome_downloader{
     // publishDir publishes the output in a specific folder with copy mode
     storeDir "${params.outdir}/reference_genome"
 
-    input:
-    val trigger from refgen_downloader
-
     output:
     file "hg38.fa" into refgen_integrate_builder_down, refgen_integrate_converter_down, refgen_referenceGenome_index_down, refgen_integrate_down, refgen_genefuse_down
 
@@ -213,8 +210,6 @@ process ericsctipt_downloader{
 
     storeDir "${params.outdir}/ericscript/files"
 
-    input:
-    val x from ch1_ericscript
 
     output:
     file "ericscript_db_homosapiens_ensembl84" into ch3_ericscript
@@ -240,18 +235,19 @@ process ericsctipt_downloader{
 process ericscript{
     tag "${pair_id}"
 
-    publishDir "${params.outdir}/ericscript", mode: 'move'
+    publishDir "${params.outdir}/ericscript/result", mode: 'move'
 
     input:
     tuple pair_id, file(rna_reads), file(ericscript_db) from rna_reads_ericscript.combine(ch2_ericscript.mix(ch3_ericscript))
 
     output:
-    file "output/${pair_id}" optional true into ericscript_fusions
+    file "output/${pair_id}" into ericscript_fusions
 
     when: params.ericscript || !(params.arriba || params.ericscript || params.fusioncatcher || params.genefuse || params.integrate)
 
     script:
     reads = "../${rna_reads[0]} ../${rna_reads[1]}" //reads = params.single_end ? rna_reads[0] : "../${rna_reads[0]} ../${rna_reads[1]}"
+    println reads
     """
     #!/bin/bash