diff fastq_dump_pe.Rmd @ 2:8e913d0be3e6 draft

planemo upload

--- a/fastq_dump_pe.Rmd	Wed Apr 04 12:55:55 2018 -0400
+++ b/fastq_dump_pe.Rmd	Wed Apr 04 13:21:37 2018 -0400
@@ -10,21 +10,18 @@
 ```
 
 
-```{bash echo=FALSE}
+```{bash}
 # build job-script
 mkdir -p ${WORKING_DIR}/paired-end-reads
-```
 
-
-```{bash}
 # paired-end.sh
 mkdir -p ${X_d}/paired-end-reads
 cat <<EOF >${X_d}/paired-end.sh
-if [ "${X_B}" ];then
+if [ "${X_A}" ];then
   fastq-dump \\
     --split-files \\
-    ${X_B} \\
-    -O ${X_d}/paired-end-reads > ${X_d}/paired-end-log.txt 2>&1
+    ${X_A} \\
+    -O ${WORKING_DIR}/paired-end-reads > ${X_d}/paired-end-log.txt 2>&1
 else
   echo "No accessions are provided" > ${X_d}/paired-end-log.txt 2>&1
 fi
@@ -48,7 +45,7 @@
 
 
 ```{bash, 'display script', results='asis', echo=FALSE}
-echo '### paired-end reads'
+echo '## Job script'
 echo ''
 echo ''
 echo '```bash'