From 3d5b1095816fe9fc24e011029a48fdbef43497c3 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 21 Jun 2020 15:10:47 -0500
Subject: [PATCH] Fix module load and ulimits

---
 workflow/main.nf | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/workflow/main.nf b/workflow/main.nf
index 18d8324..f093e3c 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -99,6 +99,7 @@ process trackStart {
   script:
   """
   hostname
+  ulimit -u 16384
   ulimit -a
   export https_proxy=\${http_proxy}
  
@@ -134,6 +135,7 @@ process checkDesignFile {
   script:
     """
     hostname
+    ulimit -u 16384
     ulimit -a
     noSpaceDesign=\$(echo "${designLocation}" | tr -d ' ')
     if [[ "\${noSpaceDesign}" != "${designLocation}" ]]; then
@@ -325,6 +327,7 @@ process count310 {
  */
 process versions {
   tag "${name}"
+  module 'python/3.6.1-2-anaconda:pandoc/2.7'
 
   input:
     file versions_pythonScript
@@ -357,6 +360,7 @@ metricsSummary = metricsSummary211.mix(metricsSummary302, metricsSummary310)
 process multiqc {
   tag "${name}"
   publishDir "${outDir}/${task.process}/${name}", mode: 'copy'
+  module 'multiqc/1.7'
 
   input:
     file ('*') from metricsSummary.collect()
@@ -368,6 +372,7 @@ process multiqc {
   script:
     """
     hostname
+    ulimit -u 16384
     ulimit -a
     awk 'FNR==1 && NR!=1{next;}{print}' *.tsv > metrics_summary_mqc.tsv
     sed -i '1s/^.*\tE/Sample\tE/' metrics_summary_mqc.tsv
-- 
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