Added two parameters to increase stringency of variant calling:

1. Changed clipping penalty parameter in bwa mem from 5 to 1.  This favors more soft-trimming at the ends of reads.  Since variants at the ends of reads are less reliable, this reduces false-positive variant calling.
2. Expanded ivar trim trimming using the -x offset parameter.  This trims extra bases around primer binding sites.  This also makes variant calling more stringent.

See these issues for more information on these settings:

nf-core/viralrecon#170

andersen-lab/ivar#88

main.nf

@@ -560,6 +560,7 @@ process bwa_align_to_refseq {
   rg=$(echo "@RG\\tID:$id\\tSM:$id"_"$sm\\tLB:$id"_"$sm\\tPL:ILLUMINA")
   
   bwa mem \
+  -L !{params.bwa_clipping_penalty} \
   -t !{params.refseq_bwa_threads} \
   -R $rg \
   !{params.refseq_fasta} !{input_fastq}  > !{sample_id}.unsorted.bam
@@ -621,6 +622,7 @@ process ivar_trim {
   """
   ivar trim \
     -i $bam \
+    -x $params.ivar_trim_offset \
     -e \
     -b $params.primer_bed \
     -p "${sample_id}.ivar_trim_unsorted" \

nextflow.config

@@ -62,17 +62,19 @@ params {
   // ------------------
   // Trimming settings
   // ------------------
-  always_trim_5p_bases = "0" 
-  always_trim_3p_bases = "0" 
-  post_trim_min_length = "30" 
+  always_trim_5p_bases  = "0" 
+  always_trim_3p_bases  = "0" 
+  post_trim_min_length  = "30" 
+  bwa_clipping_penalty  = "1"
 
   // -----------------------------------------
   // Fasta format files of primers to trim off
   // -----------------------------------------
-  primer_fasta_5p = "${refseq_dir}/swift_primers.5p.fasta"
-  primer_fasta_3p = "${refseq_dir}/swift_primers.3p.fasta"
-  primer_bed      = "${refseq_dir}/swift_v2_primers.bed"
-  ivar_trim       = false
+  primer_fasta_5p  = "${refseq_dir}/swift_primers.5p.fasta"
+  primer_fasta_3p  = "${refseq_dir}/swift_primers.3p.fasta"
+  primer_bed       = "${refseq_dir}/swift_v2_primers.bed"
+  ivar_trim        = true
+  ivar_trim_offset = "5"
 
   // -------------------------
   // Variant calling defaults