From 4dcf8a59a24a1617c89894feb43f90c9355ca689 Mon Sep 17 00:00:00 2001 From: skchronicles Date: Fri, 20 Sep 2019 15:49:15 -0400 Subject: [PATCH] Updating rule pca: severe filesystem latency can create race condition when copying over files --- Rules/initialqcrnaseq.snakefile | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/Rules/initialqcrnaseq.snakefile b/Rules/initialqcrnaseq.snakefile index 46b5f00..ef35bb0 100644 --- a/Rules/initialqcrnaseq.snakefile +++ b/Rules/initialqcrnaseq.snakefile @@ -1129,13 +1129,11 @@ rule pca: projDesc=config['project']['description'].rstrip('\n'), rver=config['bin'][pfamily]['tool_versions']['RVER'], scripts_dir=join(workpath,"Scripts"), - rscript1="pcacall.R", - rscript2="PcaReport.Rmd", + rscript1=join(workpath,"Scripts","pcacall.R"), + rscript2=join(workpath,"Scripts","PcaReport.Rmd"), shell: """ cd {params.outdir} -if [ ! -f {params.rscript1} ]; then cp {params.scripts_dir}/{params.rscript1} {params.outdir}/;fi -if [ ! -f {params.rscript2} ]; then cp {params.scripts_dir}/{params.rscript2} {params.outdir}/;fi + module load {params.rver} -Rscript {params.rscript1} '{params.outdir}' '{output.outhtml}' '{input.file1}' '{input.file2}' '{params.projectId}' '{params.projDesc}' +Rscript {params.rscript1} '{params.outdir}' '{output.outhtml}' '{input.file1}' '{input.file2}' '{params.projectId}' '{params.projDesc}' '{params.rscript2}' """ -