update config

nextflow.config

 process.executor='slurm'
 process.queue='super'
-process.clusterOptions = '--hold'
\ No newline at end of file
+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'
\ No newline at end of file

workflow/main.nf

@@ -227,7 +227,7 @@ process gatkbam {
   publishDir "$params.output", mode: 'copy'
 
   input:
-  set subjid,pair_id, file(rbam) from deduped2
+  set pair_id, file(rbam) from deduped2
 
   output:
   set file("${pair_id}.final.bam"),file("${pair_id}.final.bai") into gatkbam