Moved to FLASh for merging of read pairs

Kept unmerged reads

modules/quantify.nf

@@ -7,6 +7,7 @@ container__FAMLI = 'golob/famli2:2.0.0.pre'
 container__anndata = 'golob/python-anndata:0.9.2'
 container__diamond = 'quay.io/biocontainers/diamond:2.1.8--h43eeafb_0'
 container__vsearch = 'quay.io/biocontainers/vsearch:2.22.1--hf1761c0_0'
+container__flash = 'golob/flash:1.2.11'
 
 // Processes used for alignment of reads against gene databases
 
@@ -35,7 +36,7 @@ workflow Alignment_wf {
 
     // Align all specimens against the DIAMOND database
     Diamond(
-        MergeFastqToFasta.out,
+        MergeFastqToFasta.out[0],
         allele_dmnd,
     )
 
@@ -83,7 +84,7 @@ process DiamondDB {
 // Merge read pairs and convert to fasta:
 process MergeFastqToFasta {
     tag "Merge fastq files into fasta for alignment"
-    container "${container__vsearch}"
+    container "${container__flash}"
     label 'io_limited'
     errorStrategy 'ignore'
 
@@ -92,16 +93,21 @@ process MergeFastqToFasta {
 
     output:
         tuple val(sample_name), file("${sample_name}.fasta.gz")
+        file("${sample_name}.flash.log")
 
     """
     set -e
-    vsearch \
-        --fastq_mergepairs ${R1} \
-        --reverse ${R2} \
-        --fastaout ${sample_name}.fasta
-
+    flash \
+        ${R1} ${R2} \
+        -t ${task.cpus} \
+        --min-overlap=2 \
+        --max-overlap=65 \
+        2>&1 | tee ${sample_name}.flash.log
+    touch ${sample_name}.fasta
+    cat out.extendedFrags.fastq | awk '{if(NR%4==1) {printf(">%s\\n",substr(\$0,2));} else if(NR%4==2) print;}' >> ${sample_name}.fasta
+    cat out.notCombined_1.fastq | awk '{if(NR%4==1) {printf(">%s\\n",substr(\$0,2));} else if(NR%4==2) print;}' >> ${sample_name}.fasta
+    cat out.notCombined_2.fastq | awk '{if(NR%4==1) {printf(">%s\\n",substr(\$0,2));} else if(NR%4==2) print;}' >> ${sample_name}.fasta
     gzip ${sample_name}.fasta
-    ls -lh ${sample_name}.fasta.gz
     """
 
 }