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 -- GitLab