update process scripts

nextflow.config

+process.executor = 'slurm'
+process.queue = 'super'
+process.clusterOptions = '--hold'
+trace.enabled = true
+trace.file = 'pipeline_trace.txt'
+trace.field = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime'
+report.enable = true
+report.file= 'report.html'

workflow/main.nf

@@ -67,7 +67,7 @@ Channel
 
 process trimpe {
   errorStrategy 'ignore'
-  publishDir "$baseDir/output", mode: 'copy'
+  publishDir "$params.output", mode: 'copy'
   input:
   set famid,pair_id, file(read1), file(read2) from read
   output:

process_scripts @ 291e1c35

-Subproject commit 240f711bab848e6426e96205620f2db692da1f81
+Subproject commit 291e1c352873ce14881ab8b1822fa7d3183b946b