Update to version 0.2.0

hanielcedraz · web-flow · commit b9d5f9e73a9c · 2019-03-21T11:43:53.000-03:00
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))
 }
 
 

Original file line number	Diff line number	Diff line change
`@@ -155,7 +155,7 @@ antQC <- 'antQC'`
`155`	`155`	`if(!file.exists(file.path(antQC))) dir.create(file.path(antQC), recursive = TRUE, showWarnings = FALSE)`
`156`	`156`	`for (i in samples[,2:3]){`
`157`	`157`	`system2('fastqc',`
`158`		`- paste0('00-Fastq/', i, ' --outdir=', 'antQC/', ' -t ', length(samples)))`
	`158`	`+ paste0('00-Fastq/', i, ' --outdir=', 'antQC/', ' -t ', opt$sampleToprocs))`
`159`	`159`	`}`
`160`	`160`
`161`	`161`
`@@ -195,7 +195,7 @@ posQC <- 'posQC'`
`195`	`195`	`if(!file.exists(file.path(posQC))) dir.create(file.path(posQC), recursive = TRUE, showWarnings = FALSE)`
`196`	`196`	`for (i in samples[,1]){`
`197`	`197`	`system2('fastqc',`
`198`		`- paste0('01-trimmomatic/', i, '_trim_PE*', ' --outdir=', 'posQC/', ' -t ', length(samples)))`
	`198`	`+ paste0('01-trimmomatic/', i, '_trim_PE*', ' --outdir=', 'posQC/', ' -t ', opt$sampleToprocs))`
`199`	`199`	`}`
`200`	`200`
`201`	`201`