Update to version 0.2.0

hanielcedraz · Mar 21, 2019 · b9d5f9e · b9d5f9e
1 parent 2985381
commit b9d5f9e
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/baqcom_qc b/baqcom_qc
@@ -155,7 +155,7 @@ antQC <- 'antQC'
 if(!file.exists(file.path(antQC))) dir.create(file.path(antQC), recursive = TRUE, showWarnings = FALSE)
 for (i in samples[,2:3]){
         system2('fastqc',
-               paste0('00-Fastq/', i, ' --outdir=', 'antQC/', ' -t ', length(samples)))
+               paste0('00-Fastq/', i, ' --outdir=', 'antQC/', ' -t ', opt$sampleToprocs))
 }
 
 
@@ -195,7 +195,7 @@ posQC <- 'posQC'
 if(!file.exists(file.path(posQC))) dir.create(file.path(posQC), recursive = TRUE, showWarnings = FALSE)
 for (i in samples[,1]){
     system2('fastqc',
-            paste0('01-trimmomatic/', i, '_trim_PE*', ' --outdir=', 'posQC/', ' -t ', length(samples)))
+            paste0('01-trimmomatic/', i, '_trim_PE*', ' --outdir=', 'posQC/', ' -t ', opt$sampleToprocs))
 }