Replaced samtools view and bam2fq to extract fastq to map to hla refe…

…rence with samtools collate and samtools fastq. Now outputs gzipped fastq files and doesn't remove the intermediate files.

modules/local/yaramap.nf

@@ -25,25 +25,16 @@ process YARA_MAPPER {
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
 
     """
-    samtools view -@ ${split_cpus} -h -f 0x40 $bam > output_1.bam
-    samtools view -@ ${split_cpus} -h -f 0x80 $bam > output_2.bam
-    samtools bam2fq output_1.bam > output_1.fastq
-    samtools bam2fq output_2.bam > output_2.fastq
+    samtools collate -u -O -@ ${task.cpus} ${bam} | samtools fastq -@ ${task.cpus} -1 output_1.fastq.gz -2 output_2.fastq.gz -0 /dev/null
     yara_mapper \\
         $options.args \\
         -t ${task.cpus} \\
         -f bam \\
         ${index}/yara \\
-        output_1.fastq \\
-        output_2.fastq > output.bam
+        output_1.fastq.gz \\
+        output_2.fastq.gz > output.bam
     samtools view -@ ${split_cpus} -hF 4 -f 0x40 -b output.bam > ${prefix}_1.mapped.bam
     samtools view -@ ${split_cpus} -hF 4 -f 0x80 -b output.bam > ${prefix}_2.mapped.bam
-    
-    rm output_2.bam
-    rm output_1.bam
-    rm output_1.fastq
-    rm output_2.fastq
-    rm output.bam
 
     echo \$(yara_mapper --version) | sed "s/^.*yara_mapper version: //; s/ .*\$//" > ${software}.version.txt
     """