From 2005645ef7beb46bf1c20fdfda272e3a27c9030b Mon Sep 17 00:00:00 2001
From: Marc Hoeppner <mphoeppner@gmail.com>
Date: Mon, 28 Oct 2024 09:42:44 +0100
Subject: [PATCH] Updating jinja template

---
 assets/gabi_template.html |  5 ++---
 bin/gabi.py               | 19 ++++++++-----------
 subworkflows/mlst/main.nf |  4 +++-
 3 files changed, 13 insertions(+), 15 deletions(-)

diff --git a/assets/gabi_template.html b/assets/gabi_template.html
index c7b3801..f76081b 100644
--- a/assets/gabi_template.html
+++ b/assets/gabi_template.html
@@ -128,14 +128,13 @@ <h2>Assembly metrics</h2>
 <table>
     <tr>
         <th scope="col">Sample</th>
-        <th scope="col">Assembly size</th>
+        <th scope="col">Assembly size (Mb)</th>
         <th scope="col">Fraction of reference</th>
         <th scope="col">Ns per 100kb</th>
-        <th scope="col">Largest contig</th>
+        <th scope="col">Largest contig (Kb)</th>
         <th scope="col">Misassembled contigs</th>
         <th scope="col">Contigs > 5kb</th>
         <th scope="col">Size (Mb) in contigs > 5kb</th>
-
     </tr>
 
 {% for row in summary %}
diff --git a/bin/gabi.py b/bin/gabi.py
index c6bc826..cdf3a0a 100755
--- a/bin/gabi.py
+++ b/bin/gabi.py
@@ -8,6 +8,7 @@
 
 parser = argparse.ArgumentParser(description="Script options")
 parser.add_argument("--input", help="An input option")
+parser.add_argument("--references", help="Reference values for various taxa")
 parser.add_argument("--template", help="A JINJA2 template")
 parser.add_argument("--output")
 args = parser.parse_args()
@@ -23,9 +24,9 @@
 references = {
     "genomes" : {
         "Escherichia coli": {
-            "size": 4.8,
+            "size": 5.0,
             "max_contigs": 500,
-            "n50": 200
+            "n50": 80
         },
         "Listeria monocytogenes": {
             "size": 2.9,
@@ -87,11 +88,12 @@
 
 def main(yaml, template, output):
 
+    # Read all the JSON files we see in this folder
     json_files = [pos_json for pos_json in os.listdir('.') if pos_json.endswith('.json')]
     json_files.sort()
 
     data = {}
-    data["summary"] = [ ]
+    data["summary"] = []
 
     samples = []
 
@@ -148,15 +150,10 @@ def main(yaml, template, output):
             if taxon_perc >= 80.0:
                 taxon_status = status["pass"]
             elif taxon_perc >= 60.0:
-                taxon_status = status["warn"]
-                if (this_status == status["pass"]):
-                    this_status = status["warn"]
+                taxon_status = status["warn"]    
             else:
                 taxon_status = status["fail"]
-                # probably not an outright fail for the whole analysis
-                if (this_status == status["pass"]):
-                    this_status = status["warn"]
-
+                
             taxon_count = 0
             taxon_count_status = status["pass"]
 
@@ -218,7 +215,7 @@ def main(yaml, template, output):
             quast["duplication"] = jdata["quast"]["Duplication ratio"]
             quast["N"] = jdata["quast"]["# N's per 100 kbp"]
             quast["mismatches"] = jdata["quast"]["# mismatches per 100 kbp"]
-            quast["largest_contig"] = jdata["quast"]["Largest contig"]
+            quast["largest_contig"] = round((int(jdata["quast"]["Largest contig"])/1000),2)
             quast["misassembled"] = jdata["quast"]["# misassembled contigs"]
             quast["contigs_5k"] = jdata["quast"]["# contigs (>= 5000 bp)"]
             quast["size_5k"] = round(float(int(jdata["quast"]["Total length (>= 5000 bp)"])/1000000),2)
diff --git a/subworkflows/mlst/main.nf b/subworkflows/mlst/main.nf
index a631ab8..906f012 100644
--- a/subworkflows/mlst/main.nf
+++ b/subworkflows/mlst/main.nf
@@ -166,7 +166,9 @@ workflow MLST_TYPING {
             meta.db_name = m.db_name
             tuple(meta, a, d)
         }.groupTuple(by: [0, 2])
-        .filter { m, a, d -> a.size() > 2 }
+        .set { ch_assemblies_chewie_grouped }
+
+        ch_assemblies_chewie_grouped.filter { m, a, d -> (a.size() > 2) }
         .set { ch_assemblies_chewie_call }
 
         CHEWBBACA_ALLELECALL(