From 4e393c539ff4fd97e57b2a2077f9eb97bba93e96 Mon Sep 17 00:00:00 2001
From: Rachel Colquhoun <rachel.colquhoun@ed.ac.uk>
Date: Tue, 24 Sep 2024 17:16:10 +0100
Subject: [PATCH 1/2] fix

---
 bin/report.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/bin/report.py b/bin/report.py
index 05bf6da..aa7dcdf 100644
--- a/bin/report.py
+++ b/bin/report.py
@@ -121,8 +121,8 @@ def __init__(self, file_name=None):
         self.domains = defaultdict(int)
         if file_name:
             self.load_df(file_name)
-            self.unclassified = self.entries[0].count
-            self.classified = self.entries[1].count
+            self.unclassified = self.entries["0"].count
+            self.classified = self.entries["1"].count
             self.total = self.classified + self.unclassified
 
     def print(self):
@@ -392,4 +392,4 @@ def check_host(self, host_dict):
                 sys.stderr.write(
                     f"ERROR: found {self.entries[host_id].count} reads corresponding to host {self.entries[host_id].name} with taxon_id {host_id}, max allowed is {max_host_count}\n"
                     )
-                sys.exit(2)
\ No newline at end of file
+                sys.exit(2)

From cfe0b2292d3aa6de097d73980d9aab9ef2149ee3 Mon Sep 17 00:00:00 2001
From: Rachel Colquhoun <rachel.colquhoun@ed.ac.uk>
Date: Tue, 24 Sep 2024 17:16:51 +0100
Subject: [PATCH 2/2] version bump

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 1b9a68b..651885b 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -32,7 +32,7 @@ manifest {
     description     = 'Classify metagenomic sequence data from human respiratory infections.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=20.10.0'
-    version         = 'v1.3.0'
+    version         = 'v1.3.1'
 }
 
 profiles {