Commit 6009469b authored by psimion's avatar psimion
Browse files

saving fasta_oneline files

parent 2e7e306a
......@@ -28,7 +28,8 @@ for ref in "${orders[@]}"; do
# setting fastq files (paired/unpaired and zipped/unzipped)
if [ $MODE == "u" ]; then
if [[ "$InfosCtg" == *".gz" ]]; then
fastq="<(zcat "$INDIR"/"`echo $InfosCtg | cut -d';' -f2`")"
gunzip -c "$INDIR/"`echo $InfosCtg | cut -d';' -f2` > "$out/"`echo $InfosCtg | cut -d';' -f2`".gunziped"
fastq=$INDIR"/"`echo $InfosCtg | cut -d';' -f2`".gunziped"
else
fastq=$INDIR"/"`echo $InfosCtg | cut -d';' -f2`
fi
......
......@@ -28,7 +28,8 @@ for ref in "${orders[@]}"; do
# setting fastq files (paired/unpaired and zipped/unzipped)
if [ $MODE == "u" ]; then
if [[ "$InfosCtg" == *".gz" ]]; then
fastq="<(zcat "$INDIR"/"`echo $InfosCtg | cut -d';' -f2`")"
gunzip -c "$INDIR/"`echo $InfosCtg | cut -d';' -f2` > "$out/"`echo $InfosCtg | cut -d';' -f2`".gunziped"
fastq=$INDIR"/"`echo $InfosCtg | cut -d';' -f2`".gunziped"
else
fastq=$INDIR"/"`echo $InfosCtg | cut -d';' -f2`
fi
......
......@@ -29,8 +29,7 @@ elif [ $OUTPUTLEVEL == "2" ]; then
done
# miscellaneous
mv $out/*.list $out/utility_files_CroCo
rm -f $out/*.fasta.oneline
mv $out/*.list $out/*.fasta.oneline $out/utility_files_CroCo
else echo -e "\nwarning : output level value must be set to either '1' or '2' (default = '2')"
fi
......
......@@ -29,8 +29,7 @@ elif [ $OUTPUTLEVEL == "2" ]; then
done
# miscellaneous
mv $out/*.list $out/utility_files_CroCo
rm -f $out/*.fasta.oneline
mv $out/*.list $out/*.fasta.oneline $out/utility_files_CroCo
else echo -e "\nwarning : output level value must be set to either '1' or '2' (default = '2')"
fi
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment