metaWRAP binning module skips BAM output if multiple pairs of fastqs with same file names are given

[Prunoideae]

I wrote a script to automate script the process of the metagenomic samples from 10+ sites. So for each direct output of read_qc, they will have a pair of fastqs at clean_reads/{sample_name}/final_pure_reads_{1/2}.fq (I know that there's a step of reassigning files with sample names in the usage tutorial, but I didn't expect it will have an effect later).

So all reads given have the same final_pure_reads as prefix, but from

metaWRAP/bin/metawrap-modules/binning.sh

Lines 220 to 244 in c4a23f0

	for num in "$@"; do
	# paired end reads
	if [ $read_type = paired ]; then
	if [[ $num == *"_1.fastq"* ]]; then
	reads_1=$num
	reads_2=${num%_*}_2.fastq
	if [ ! -s $reads_1 ]; then error "$reads_1 does not exist. Exiting..."; fi
	if [ ! -s $reads_2 ]; then error "$reads_2 does not exist. Exiting..."; fi
	tmp=${reads_1##*/}
	sample=${tmp%_*}
	if [[ ! -f ${out}/work_files/${sample}.bam ]]; then
	comm "Aligning $reads_1 and $reads_2 back to assembly"
	bwa mem -v 1 -t $threads ${out}/work_files/assembly.fa $reads_1 $reads_2 > ${out}/work_files/${sample}.sam
	if [[ $? -ne 0 ]]; then error "Something went wrong with aligning $reads_1 and $reads_2 reads to the assembly. Exiting"; fi
	comm "Sorting the $sample alignment file"
	samtools sort -T ${out}/work_files/tmp-samtools -@ $threads -O BAM -o ${out}/work_files/${sample}.bam ${out}/work_files/${sample}.sam
	if [[ $? -ne 0 ]]; then error "Something went wrong with sorting the alignments. Exiging..."; fi
	rm ${out}/work_files/${sample}.sam
	else
	comm "skipping aligning $sample reads to assembly because ${out}/work_files/${sample}.bam already exists."
	fi
	fi

We see that all samples are distinguished by their file name prefixes. So, all subsequent fastq pairs will be skipped as the final_pure_reads.bam is present.

I think this should be worth an error showing that the same file names are not permitted, at least, or it can be fixed by using something to hash the whole path (or simply, just the order it runs in the iteration like 0, 1, 2...) and make that bam the file name instead.