From 94f88adbfdb3a74c40557a2b1e974f143597b1ea Mon Sep 17 00:00:00 2001
From: taranewman <69013600+taranewman@users.noreply.github.com>
Date: Wed, 10 Apr 2024 09:09:46 -0700
Subject: [PATCH] Matrix table fix (#7)

* fix gubbins error with 2 isolates

* clean spaces

* use run gubbins boolean

* clean white space
---
 main.nf                | 13 ++++++++++---
 modules/gubbins.nf     |  6 ++++++
 modules/snippy_core.nf | 13 ++++++++++++-
 3 files changed, 28 insertions(+), 4 deletions(-)

diff --git a/main.nf b/main.nf
index 43f4ea6..ee30ed6 100644
--- a/main.nf
+++ b/main.nf
@@ -26,17 +26,24 @@ workflow {
     ch_mask = Channel.fromPath(params.mask)
   }
 
+  
+
   main:
 
   snippy_core(ch_snippy_dirs.collect().combine(ch_ref).map{ it -> [it[0..-2], it[-1]] }.combine(ch_mask))
 
+  
   if (!params.skip_gubbins) {
-    gubbins(snippy_core.out.clean_full_alignment)
-    ch_alignment = gubbins.out.filtered_polymorphic_sites
+    gubbins(snippy_core.out.clean_full_alignment, snippy_core.out.run_gubbins)
+    if (snippy_core.out.run_gubbins == "true") {
+      ch_alignment = gubbins.out.filtered_polymorphic_sites
+    } else {
+      ch_alignment = snippy_core.out.clean_full_alignment
+    }
   } else {
     ch_alignment = snippy_core.out.clean_full_alignment
   }
-
+  
   snp_sites(ch_alignment)
 
   iqtree(snp_sites.out)
diff --git a/modules/gubbins.nf b/modules/gubbins.nf
index ce4cb30..b1de688 100644
--- a/modules/gubbins.nf
+++ b/modules/gubbins.nf
@@ -1,15 +1,21 @@
 process gubbins {
+  
+  errorStrategy 'ignore'
 
   publishDir "${params.outdir}", mode: 'copy', pattern: "gubbins.*"
 
   input:
   path(alignment)
+  val(run_gubbins)
 
   output:
   path('gubbins.filtered_polymorphic_sites.fasta'), emit: filtered_polymorphic_sites
   path('gubbins.recombination_predictions.gff'),    emit: recombination_predictions_gff
   path('gubbins.per_branch_statistics.tsv'),        emit: per_branch_statistics
 
+  when:
+  run_gubbins == "true"
+
   script:
   """
   run_gubbins.py \
diff --git a/modules/snippy_core.nf b/modules/snippy_core.nf
index 2e17642..b521c6d 100644
--- a/modules/snippy_core.nf
+++ b/modules/snippy_core.nf
@@ -12,6 +12,8 @@ process snippy_core {
     path('core.tsv'), emit: core_stats
     path('core.full.aln'), emit: full_alignment
     path('clean.full.aln'), emit: clean_full_alignment
+    val('run_gubbins'), emit: run_gubbins
+
 
     script:
     """
@@ -23,5 +25,14 @@ process snippy_core {
     snippy-clean_full_aln core.full.aln > clean.full.aln
 
     add_percent_used.py core.txt > core.tsv
+
+    num_isolates=\$(echo "\$snippy_dirs" | tr -s ' ' | wc -w)
+    if [ "\$num_isolates" -ge 3 ]; then
+        run_gubbins='true'
+    else
+        run_gubbins='false'
+    fi
+    
     """
-}
\ No newline at end of file
+}
+