comparison shell-script-template.sh @ 6:5b07e567864b draft

planemo upload commit ee93fa730d90ffc1a895a849bdcb6050ed5ad2c9-dirty

5:2c663ddb8488

# SHELL_SCRIPT file name
SHELL_SCRIPT='skewer.sh'

# run SHELL_SCRIPT within tool outputs directory
cd ${REPORT_FILES_PATH}

# build job-script.sh
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 
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}

rm temp.sh

# run SHELL_SCRIPT
sh ${SHELL_SCRIPT}

# rename log file
if [ -e trim-trimmed.log ]; then
  cp trim-trimmed.log trim-trimmed.txt
fi

6:5b07e567864b

# run SHELL_SCRIPT within tool outputs directory
cd ${REPORT_FILES_PATH}

#--------- index genome --------
# create genome directory for genome indexes
mkdir -p ${X_d}/genomeDir

cat >temp.sh <<EOF
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

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

#----- SAM to sorted BAM ------
echo "samtools sort -o Aligned.out.sorted.bam Aligned.out.sam" > sam2bam.sh
sh sam2bam.sh

#----- evaluate mapping -------
echo "samtools flagstat Aligned.out.sorted.bam > flagstat.txt" > flagstat.sh
sh flagstat.sh