Apply samtools fixmate after ivar trim

CHANGELOG.md

@@ -11,11 +11,13 @@ Special thanks to the following for their code contributions to the release:
 
 - [Adam Talbot](https://github.com/adamrtalbot)
 - [Joon Klaps](https://github.com/Joon-Klaps)
+- [Jessica Wu](https://github.com/wutron)
 
 Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
 
 ### Enhancements & fixes
 
+- [[PR #396](https://github.com/nf-core/viralrecon/pull/396)] - Apply samtools fixmate after ivar trim
 - [[#299](https://github.com/nf-core/viralrecon/issues/299)] - Add the freyja pipeline as a subworkflow
 - [[PR #387](https://github.com/nf-core/viralrecon/pull/387)] - Software closes gracefully when encountering an error
 - [[PR #395](https://github.com/nf-core/viralrecon/pull/395)] - Remove minia from default assemblers because it is unreliable

conf/modules_illumina.config

@@ -240,6 +240,20 @@ if (!params.skip_variants) {
                 ]
             }
 
+            withName: '.*:.*:BAM_TRIM_PRIMERS_IVAR:SAMTOOLS_COLLATE' {
+                ext.prefix = { "${meta.id}.ivar_trim.collate" }
+                publishDir = [ enabled:false ]
+            }
+
+            withName: '.*:.*:BAM_TRIM_PRIMERS_IVAR:SAMTOOLS_FIXMATE' {
+                ext.prefix = { "${meta.id}.ivar_trim" }
+                publishDir = [
+                    path: { "${params.outdir}/variants/bowtie2" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.bam"
+                ]
+            }
+
             withName: '.*:.*:BAM_TRIM_PRIMERS_IVAR:.*:SAMTOOLS_SORT' {
                 ext.prefix = { "${meta.id}.ivar_trim.sorted" }
                 publishDir = [

subworkflows/local/bam_trim_primers_ivar.nf

@@ -4,6 +4,8 @@
 
 include { IVAR_TRIM               } from '../../modules/nf-core/ivar/trim/main'
 include { BAM_SORT_STATS_SAMTOOLS } from '../nf-core/bam_sort_stats_samtools/main'
+include { SAMTOOLS_COLLATE        } from '../../modules/nf-core/samtools/collate/main'
+include { SAMTOOLS_FIXMATE        } from '../../modules/nf-core/samtools/fixmate/main'
 
 workflow BAM_TRIM_PRIMERS_IVAR {
     take:
@@ -24,17 +26,26 @@ workflow BAM_TRIM_PRIMERS_IVAR {
     )
     ch_versions = ch_versions.mix(IVAR_TRIM.out.versions.first())
 
+    //
+    // samtools fixmate fills in mate coordinates and insert size fields
+    //
+    SAMTOOLS_COLLATE ( IVAR_TRIM.out.bam, fasta )
+    ch_versions = ch_versions.mix(SAMTOOLS_COLLATE.out.versions.first())
+
+    SAMTOOLS_FIXMATE ( SAMTOOLS_COLLATE.out.bam )
+    ch_versions = ch_versions.mix(SAMTOOLS_FIXMATE.out.versions.first())
+
     //
     // Sort, index BAM file and run samtools stats, flagstat and idxstats
     //
     BAM_SORT_STATS_SAMTOOLS (
-        IVAR_TRIM.out.bam,
+        SAMTOOLS_FIXMATE.out.bam,
         fasta
     )
     ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS.out.versions)
 
     emit:
-    bam_orig = IVAR_TRIM.out.bam                    // channel: [ val(meta), bam   ]
+    bam_orig = SAMTOOLS_FIXMATE.out.bam             // channel: [ val(meta), bam   ]
     log_out  = IVAR_TRIM.out.log                    // channel: [ val(meta), log   ]
 
     bam      = BAM_SORT_STATS_SAMTOOLS.out.bam      // channel: [ val(meta), [ bam ] ]