Stripe extra .fastq extension form bowtie call

donald · Sep 13, 2022 · 70df2e4 · 70df2e4
1 parent 3620e72
commit 70df2e4
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/Adapting_new_script_for_computing_cluster.sh b/Adapting_new_script_for_computing_cluster.sh
@@ -97,7 +97,7 @@ execute() {
 
 	: Mapping $id with bowtie2
 
-	bowtie2 --very-sensitive-local --no-mixed -p $THREADS --no-discordant --phred33 -I 10 -X 2000 -x $ebwt -1 ${f1}_val_1.fq -2 ${f2}_val_2.fq \
+	bowtie2 --very-sensitive-local --no-mixed -p $THREADS --no-discordant --phred33 -I 10 -X 2000 -x $ebwt -1 ${f1%%.fastq}_val_1.fq -2 ${f2%%.fastq}_val_2.fq \
 			-S $id.sam >> $id\.mappingStats.txt 2>&1
 
 	: Creating BAM files for $id and filtering for paired and mapped reads