Commit d1beea79 authored by Brandi Cantarel's avatar Brandi Cantarel

update config

parent 863e86e3
Pipeline #1669 failed with stage
in 1000 minutes
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
......@@ -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
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment