Let submitter parse input file name patterns

Adapting_new_script_for_computing_cluster.sh

@@ -33,15 +33,32 @@ usage() {
 
 submit() {
 	mkdir -p $log_dir
-	for id in $(cd $fastq_dir && ls *.fastq | rev | cut -c 9- | rev | uniq); do
-		"${MXQSUB[@]}" --stdout "$log_dir/$id.out" "$0" --execute "$id"
+	shopt -s nullglob
+
+	# input files "blabla_R_1.fastq" , "blabla_R_2.fastq"
+	#
+	#   --> id "blabla_R"     ( "_R" included for historical reasons )
+	#   --> f1 "blabla_R_1.fastq"
+	#   --> f2 "blabla_R_2.fastq"
+	#
+	for f1 in $fastq_dir/*_R_1.fastq; do
+		id=$(basename ${f1%%_1.fastq})00
+		f1=${id}_1.fastq
+		f2=${id}_2.fastq
+		if [ ! -e $fastq_dir/$f2 ]; then
+			echo "no _2.fastq file for $f1"
+			continue
+		fi
+		"${MXQSUB[@]}" --stdout "$log_dir/$id.out" "$0" --execute "$id" "$f1" "$f2"
 	done
 }
 
 execute() {
 	set -xe
 
 	id="$1"
+	f1="$2"
+	f2="$3"
 
 	cd $MXQ_JOB_TMPDIR
 
@@ -54,16 +71,16 @@ execute() {
 
 	: Running FastQC on $id 
 
-	/project/RNAseq_Mdl_data/Konrad/FastQC/fastqc fastq/${id}_1.fastq --outdir fastqc
-	/project/RNAseq_Mdl_data/Konrad/FastQC/fastqc fastq/${id}_2.fastq --outdir fastqc
+	/project/RNAseq_Mdl_data/Konrad/FastQC/fastqc fastq/$f1 --outdir fastqc
+	/project/RNAseq_Mdl_data/Konrad/FastQC/fastqc fastq/$f2 --outdir fastqc
 
 	: Trimming $id with trim_galore
 
-	prun python3 trim_galore --paired --nextera -j $THREADS fastq/${id}_1.fastq fastq/${id}_2.fastq >> $id.trimmingStats.txt 2>&1
+	prun python3 trim_galore --paired --nextera -j $THREADS fastq/$f1.fastq fastq/$f2.fastq >> $id.trimmingStats.txt 2>&1
 
 	: Mapping $id with bowtie2
 
-	bowtie2 --very-sensitive-local --no-mixed -p $THREADS --no-discordant --phred33 -I 10 -X 2000 -x $ebwt -1 ${id}_1_val_1.fq -2 ${id}_2_val_2.fq \
+	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 \
 			-S $id.sam >> $id\.mappingStats.txt 2>&1
 
 	: Creating BAM files for $id and filtering for paired and mapped reads
@@ -125,8 +142,8 @@ cp dedup_peaks/* $work_dir/dedup_peaks
 
 if [ $# = 1 -a "$1" = --submit ]; then
 	submit
-elif [ $# = 2 -a "$1" = --execute ]; then
-	execute "$2"
+elif [ $# = 4 -a "$1" = --execute ]; then
+	execute "$2" "$3" "$4"
 else
 	usage
 fi