From 565cbb58ab7ed88be6b528e2fec95b94e969485e Mon Sep 17 00:00:00 2001
From: tives82 <tiverson@utah.gov>
Date: Tue, 9 Apr 2024 14:23:06 -0600
Subject: [PATCH] Update IRMA output settings and refine Abricate flu B
 classification

---
 modules/local/abricate_flu.nf | 14 ++++++++++----
 modules/local/irma.nf         |  4 ++--
 2 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/modules/local/abricate_flu.nf b/modules/local/abricate_flu.nf
index e12763b..d7819ff 100755
--- a/modules/local/abricate_flu.nf
+++ b/modules/local/abricate_flu.nf
@@ -75,9 +75,13 @@ process ABRICATE_FLU {
 
     # Find INSaFLU subtype if Type B
     if grep -q "Type_B" $abricate_type; then
-        if grep -q "Victoria" ${meta.id}_abricate_hits.tsv; then
+        # Check for Victoria with hemagglutinin or neuraminidase or both
+        if (grep -q "Victoria" ${meta.id}_abricate_hits.tsv && grep -q "hemagglutinin" ${meta.id}_abricate_hits.tsv) || \
+            (grep -q "Victoria" ${meta.id}_abricate_hits.tsv && grep -q "neuraminidase" ${meta.id}_abricate_hits.tsv); then
             echo "Victoria" > $abricate_subtype
-        elif grep -q "Yamagata" ${meta.id}_abricate_hits.tsv; then
+        # Check for Yamagata with hemagglutinin or neuraminidase or both
+        elif (grep -q "Yamagata" ${meta.id}_abricate_hits.tsv && grep -q "hemagglutinin" ${meta.id}_abricate_hits.tsv) || \
+            (grep -q "Yamagata" ${meta.id}_abricate_hits.tsv && grep -q "neuraminidase" ${meta.id}_abricate_hits.tsv); then
             echo "Yamagata" > $abricate_subtype
         else
             echo "No abricate subtype" > $abricate_subtype
@@ -114,10 +118,12 @@ process ABRICATE_FLU {
         elif grep -q "H10" ${meta.id}_abricate_hits.tsv && grep -q "N8" ${meta.id}_abricate_hits.tsv; then
             echo "H10N8" > $abricate_subtype
     # Victoria
-        elif grep -q "Victoria" ${meta.id}_abricate_hits.tsv; then
+        elif (grep -q "Victoria" ${meta.id}_abricate_hits.tsv && grep -q "hemagglutinin" ${meta.id}_abricate_hits.tsv) || \
+            (grep -q "Victoria" ${meta.id}_abricate_hits.tsv && grep -q "neuraminidase" ${meta.id}_abricate_hits.tsv); then
             echo "Victoria" > $abricate_subtype
     # Yamagata
-        elif grep -q "Yamagata" ${meta.id}_abricate_hits.tsv; then
+        elif (grep -q "Yamagata" ${meta.id}_abricate_hits.tsv && grep -q "hemagglutinin" ${meta.id}_abricate_hits.tsv) || \
+            (grep -q "Yamagata" ${meta.id}_abricate_hits.tsv && grep -q "neuraminidase" ${meta.id}_abricate_hits.tsv); then
             echo "Yamagata" > $abricate_subtype
         else
             echo "No abricate subtype" > $abricate_subtype
diff --git a/modules/local/irma.nf b/modules/local/irma.nf
index 6afb89e..bcdd09f 100755
--- a/modules/local/irma.nf
+++ b/modules/local/irma.nf
@@ -10,8 +10,8 @@ process IRMA {
 
     output:
     tuple val(meta), path("${meta.id}/")               , emit: irma
-    tuple val(meta), path("${meta.id}/*.bam")          , emit: irma_bam
-    tuple val(meta), path("${meta.id}/*.fasta")        , emit: irma_fasta
+    tuple val(meta), path("${meta.id}/*.bam")          , optional:true, emit: irma_bam
+    tuple val(meta), path("${meta.id}/*.fasta")        , optional:true, emit: irma_fasta
     tuple val(meta), path("*.irma.consensus.fasta")    , optional:true, emit: assembly
     tuple val(meta), path("*_LOW_ABUNDANCE.txt")       , optional:true, emit: failed_assembly
     tuple val(meta), path("*_HA.fasta")                , optional:true, emit: HA