changeset 9:39831b70aabb draft

planemo upload for repository https://github.com/feltus/BDSS

--- a/rmarkdown_report.Rmd	Tue Jun 12 11:41:41 2018 -0400
+++ b/rmarkdown_report.Rmd	Tue Jun 12 12:12:56 2018 -0400
@@ -1,5 +1,5 @@
 ---
-title: 'Aurora Tool Report'
+title: 'BDSS download from SRA'
 output:
     html_document:
       highlight: pygments
@@ -53,7 +53,7 @@
 # ADD YOUR DATA ANALYSIS CODE AND MARKUP TEXT BELOW TO EXTEND THIS R MARKDOWN FILE
 ---
 
-# Download and extract reads
+# Job script
 
 ```{r echo=FALSE}
 # create two directories to store downloaded data
@@ -83,7 +83,6 @@
     } else {
       command = paste0('fastq-dump -O ', se_dir, ' ', id, '.sra')
     }
-    cat('----convert SRA to fastq/fasta------\n')
     command_stdout = system(command, intern = TRUE)
     write(command_stdout, file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/fastq-dump.log.txt'), append = TRUE)
 }
@@ -107,7 +106,6 @@
     } else {
       command = paste0('fastq-dump --split-files -O ', pe_dir, ' ', id, '.sra')
     }
-    cat('----convert SRA to fastq/fasta------\n')
     command_stdout = system(command, intern = TRUE)
     write(command_stdout, file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/fastq-dump.log.txt'), append = TRUE)
     # if(!(paste0(id, '_2.', opt$X_f) %in% list.files('pe_read_files_dir'))) {
@@ -118,8 +116,6 @@
     
 }
 
-
-cat('-----Renaming files------\n')
 # rename files for paired end reads
 old_files = list.files(path = pe_dir, full.names = TRUE)
 new_files = gsub('_1', '_forward', old_files)