diff shell-script-template.sh @ 8:7c9170b7d9f6 draft

planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311

--- a/shell-script-template.sh	Thu Apr 26 12:49:35 2018 -0400
+++ b/shell-script-template.sh	Thu Apr 26 13:38:15 2018 -0400
@@ -1,48 +1,47 @@
-# SHELL_SCRIPT file name
-SHELL_SCRIPT='skewer.sh'
-
 # run SHELL_SCRIPT within tool outputs directory
 cd ${REPORT_FILES_PATH}
 
-# build job-script.sh
+#--------- index genome --------
+# create genome directory for genome indexes
+mkdir -p ${X_d}/genomeDir
+
 cat >temp.sh <<EOF
-skewer \\
-	${X_A} \\
-	${X_B} \\
-	-x ${X_x} \\ 
-	-y ${X_y} \\
-	-m ${X_m} \\
-	-r ${X_r} \\
-	-d ${X_D} \\
-	-q ${X_q} \\
-	-Q ${X_Q} \\
-	-l ${X_l} \\
-	-j ${X_j} \\
-	-M ${X_M} \\
-	-b ${X_b} \\
-	-c ${X_b} \\
-	-n ${X_n} \\
-	-u ${X_u} \\
-	-f ${X_f} \\
-	-z ${X_z} \\
-	-qiime ${X_E} \\
-	-quiet ${X_F} \\
-	-i ${X_i} \\
-	-o trim > /dev/null 2>&1 
+STAR \\
+  --runMode genomeGenerate \\
+  --genomeDir ${X_d}/genomeDir \\
+  --genomeFastaFiles $( echo ${X_A} | sed 's/,/ /g' ) \\
+  --sjdbGTFfile ${X_B} \\
+  --sjdbOverhang ${X_C} \\
+  > /dev/null 2>&1
 EOF
 
-# remove empty input lines
-grep -v '\-M  \\' temp.sh |\
-  grep -v 'None' |\
-  grep -v 'NO_ARGUMENT_NO' |\
-  sed 's/NO_ARGUMENT_YES//g' > ${SHELL_SCRIPT}
+grep -v None temp.sh > index-genome.sh
+
+# run star
+sh index-genome.sh
 
+#---- mapping ---------
+cat >temp.sh <<EOF
+STAR \\
+  --genomeDir ${X_d}/genomeDir \\
+  --readFilesIn \\
+  ${X_F} \\
+  ${X_R} \\
+  > /dev/null 2>&1
+EOF
+
+grep -v None temp.sh > mapping.sh
+
+# run mapping
+sh mapping.sh
+
+# remove temp.sh
 rm temp.sh
 
-# run SHELL_SCRIPT
-sh ${SHELL_SCRIPT}
+#----- SAM to sorted BAM ------
+echo "samtools sort -o Aligned.out.sorted.bam Aligned.out.sam" > sam2bam.sh
+sh sam2bam.sh
 
-# rename log file
-if [ -e trim-trimmed.log ]; then
-  cp trim-trimmed.log trim-trimmed.txt
-fi
\ No newline at end of file
+#----- evaluate mapping -------
+echo "samtools flagstat Aligned.out.sorted.bam > flagstat.txt" > flagstat.sh
+sh flagstat.sh