From 0bbaa71badc6f384428a685c7c5d28602ccd6346 Mon Sep 17 00:00:00 2001
From: Clea Siguret <clea.siguret@gmail.com>
Date: Fri, 27 Sep 2024 09:46:45 +0200
Subject: [PATCH 1/3] Fix test for shovill_contigs_graph

---
 .../genome-assembly/bacterial-genome-assembly/CHANGELOG.md  | 6 ++++++
 .../bacterial_genome_assembly-tests.yml                     | 4 ++--
 .../bacterial-genome-assembly/bacterial_genome_assembly.ga  | 2 +-
 3 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md b/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md
index 76ccd6b1b..8f8cc201c 100644
--- a/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md
+++ b/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md
@@ -1,5 +1,11 @@
 # Changelog
 
+## [1.1.3] 2024-09-27
+
+### Manual update
+
+- Changed 'shovill_contigs_graph' test in bacterial_genome_assembly-tests.yml
+
 ## [1.1.2] 2024-09-19
 
 ### Manual update
diff --git a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly-tests.yml b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly-tests.yml
index b184f0a50..c85eba22b 100644
--- a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly-tests.yml
+++ b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly-tests.yml
@@ -11,8 +11,8 @@
   outputs:
     shovill_contigs_graph:
       assert:
-        has_n_lines:
-          n: 18
+        has_text:
+          text: "KC:i"
     shovill_logfile:
       assert:
         has_text:
diff --git a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga
index f9b1fd302..75730ec75 100644
--- a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga
+++ b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga
@@ -26,7 +26,7 @@
         }
     ],
     "format-version": "0.1",
-    "release": "1.1.2",
+    "release": "1.1.3",
     "license": "GPL-3.0-or-later",
     "name": "Bacterial Genome Assembly using Shovill",
     "steps": {

From 556092614d6b1c22d5b107c2c88021872c1fcefe Mon Sep 17 00:00:00 2001
From: Clea Siguret <clea.siguret@gmail.com>
Date: Fri, 27 Sep 2024 09:59:41 +0200
Subject: [PATCH 2/3] Removed 1.1.3 bump

---
 .../genome-assembly/bacterial-genome-assembly/CHANGELOG.md  | 6 ------
 .../bacterial-genome-assembly/bacterial_genome_assembly.ga  | 2 +-
 2 files changed, 1 insertion(+), 7 deletions(-)

diff --git a/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md b/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md
index 8f8cc201c..76ccd6b1b 100644
--- a/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md
+++ b/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md
@@ -1,11 +1,5 @@
 # Changelog
 
-## [1.1.3] 2024-09-27
-
-### Manual update
-
-- Changed 'shovill_contigs_graph' test in bacterial_genome_assembly-tests.yml
-
 ## [1.1.2] 2024-09-19
 
 ### Manual update
diff --git a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga
index 75730ec75..f9b1fd302 100644
--- a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga
+++ b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga
@@ -26,7 +26,7 @@
         }
     ],
     "format-version": "0.1",
-    "release": "1.1.3",
+    "release": "1.1.2",
     "license": "GPL-3.0-or-later",
     "name": "Bacterial Genome Assembly using Shovill",
     "steps": {

From 62a3cf95a2ec521430499ad5889b47e5a5c3cea7 Mon Sep 17 00:00:00 2001
From: Clea Siguret <clea.siguret@gmail.com>
Date: Fri, 27 Sep 2024 10:04:03 +0200
Subject: [PATCH 3/3] Fix test syntax

---
 .../bacterial_genome_assembly-tests.yml          | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly-tests.yml b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly-tests.yml
index c85eba22b..8f9012b89 100644
--- a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly-tests.yml
+++ b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly-tests.yml
@@ -10,41 +10,41 @@
       filetype: fastqsanger.gz
   outputs:
     shovill_contigs_graph:
-      assert:
+      asserts:
         has_text:
           text: "KC:i"
     shovill_logfile:
-      assert:
+      asserts:
         has_text:
           text: "[shovill] Done."
     shovill_contigs_fasta:
-      assert:
+      asserts:
         has_text:
           text: ">contig00001"
     quast_report_tabular:
-      assert:
+      asserts:
         has_n_columns:
           n: 2
         has_text:
           text: "shovill_contigs_fasta"
     quast_log:
-      assert:
+      asserts:
         has_text:
           text: "Thank you for using QUAST!"
     refseqmasher_report_tabular:
-      assert:
+      asserts:
         has_text:
           text: "Enterococcus faecalis"
         has_n_columns:
           n: 21
     bandage_contig_graph_stats:
-      assert:
+      asserts:
         has_text:
           text: "Total length orphaned nodes (bp):"
         has_n_columns:
           n: 2
     tooldistillator_summarize:
-      assert:
+      asserts:
         has_text:
           text: "\"Assembly\": \"shovill_contigs_fasta\""
         has_text: