From d1beea79a666a4ee9aea1beacceb8843ea033c9e Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 16 Mar 2018 15:10:46 -0500
Subject: [PATCH] update config
---
nextflow.config | 7 ++++++-
workflow/main.nf | 2 +-
2 files changed, 7 insertions(+), 2 deletions(-)
diff --git a/nextflow.config b/nextflow.config
index da9f744..08ca591 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,3 +1,8 @@
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
diff --git a/workflow/main.nf b/workflow/main.nf
index 3b3031e..dee4492 100644
--- a/workflow/main.nf
+++ b/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
--
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