From fb13895fbb1f00eced179a5f876bd38e6b6cd44d Mon Sep 17 00:00:00 2001
From: Erin Young <erin.olde@gmail.com>
Date: Thu, 2 Mar 2023 12:30:11 -0700
Subject: [PATCH] fixed fastani bug

---
 modules/fastani.nf                    | 2 +-
 subworkflows/phylogenetic_analysis.nf | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/fastani.nf b/modules/fastani.nf
index 58ac9c3..145b415 100644
--- a/modules/fastani.nf
+++ b/modules/fastani.nf
@@ -47,6 +47,6 @@ process fastani {
     cat fastani/!{sample}.txt | sed 's/,//g' | sed 's/!{genomes}\\///g' | tr "\\t" "," | awk -v sample=!{sample} '{ print sample "," $0 }' >> fastani/!{sample}_fastani.csv
 
     top_hit=$(head -n 2 fastani/!{sample}_fastani.csv | tail -n 1 | cut -f 3 -d , )
-    if [ -f "$top_hit" ]; then mkdir -p top_hit ; cp $top_hit top_hit/. ; fi
+    if [ -f "!{genomes}/$top_hit" ]; then mkdir -p top_hit ; cp !{genomes}/$top_hit top_hit/. ; fi
   '''
 }
diff --git a/subworkflows/phylogenetic_analysis.nf b/subworkflows/phylogenetic_analysis.nf
index 46d0cc3..826b813 100644
--- a/subworkflows/phylogenetic_analysis.nf
+++ b/subworkflows/phylogenetic_analysis.nf
@@ -14,12 +14,12 @@ workflow phylogenetic_analysis {
     for_prokka = Channel.empty()
     if (params.extras) {
       ch_top_hit
-        .map { it -> tuple( it[0] , [ it[1].split("/")[1].split("_")[0], it[1].split("/")[1].split("_")[1]] )}
+        .map { it -> tuple( it[0] , [ it[1].split("_")[0], it[1].split("_")[1]] )}
         .set { ch_organism }
 
       if ( params.fastani_include ) {
         ch_top_hit
-          .map { it -> tuple( it[1].split("/")[1].split("_", 3)[2].replaceAll(~/.fna/,""), it[2], it[1].split("/")[1].split("_")[0, 1]) }
+          .map { it -> tuple( it[1].split("_", 3)[2].replaceAll(~/.fna/,""), it[2], it[1].split("_")[0, 1]) }
           .groupTuple(by: 0)
           .map { it -> tuple( it[0], it[1][0], it[2][0] ) }
           .unique()