From 321de3084069435731da560c37a2ba6e6ce2d52a Mon Sep 17 00:00:00 2001
From: Usman Rashid <usman@smme.edu.pk>
Date: Wed, 28 Feb 2024 11:22:15 +1300
Subject: [PATCH] Fixed reporting issues

---
 bin/assemblyqc.py                             |  7 ++++-
 bin/report_modules/parsers/params_parser.py   | 29 ++-----------------
 .../templates/params/contents.html            |  2 +-
 lib/WorkflowAssemblyqc.groovy                 |  4 +++
 modules/local/createreport.nf                 | 19 +++++++++---
 workflows/assemblyqc.nf                       |  3 +-
 6 files changed, 31 insertions(+), 33 deletions(-)

diff --git a/bin/assemblyqc.py b/bin/assemblyqc.py
index 99eb2d73..fc42eeed 100755
--- a/bin/assemblyqc.py
+++ b/bin/assemblyqc.py
@@ -27,7 +27,10 @@
 from report_modules.parsers.circos_parser import parse_circos_folder
 
 if __name__ == "__main__":
-    params_dict, params_table = parse_params_json()
+    params_dict, params_table = parse_params_json("params_json.json")
+    params_summary_dict, params_summary_table = parse_params_json(
+        "params_summary_json.json"
+    )
     tools_dict, tools_table = parse_tools_yaml()
 
     data_from_tools = {}
@@ -51,6 +54,8 @@
     data_from_tools = {
         "PARAMS_DICT": params_dict,
         "PARAMS_TABLE": params_table,
+        "PARAMS_SUMMARY_DICT": params_summary_dict,
+        "PARAMS_SUMMARY_TABLE": params_summary_table,
         "TOOLS_DICT": tools_dict,
         "TOOLS_TABLE": tools_table,
         "VERSIONS": {
diff --git a/bin/report_modules/parsers/params_parser.py b/bin/report_modules/parsers/params_parser.py
index bf07dc5a..7806f18f 100644
--- a/bin/report_modules/parsers/params_parser.py
+++ b/bin/report_modules/parsers/params_parser.py
@@ -12,32 +12,9 @@ def highlight_json(json_string):
     return highlight(json_string, lexer, formatter)
 
 
-def format_params_dict(json_dict):
-    formatted_dict = {}
-    for key, value in json_dict.items():
-        if key in ["max_cpus", "max_memory", "max_time"]:
-            continue
-
-        if not isinstance(value, dict):
-            formatted_dict[key] = value
-            continue
-
-        if "skip" in value.keys():
-            if value["skip"] == 1:
-                formatted_dict[key] = "Skipped"
-                continue
-
-        formatted_dict[key] = value
-        formatted_dict[key].pop("skip", None)
-
-    return formatted_dict
-
-
-def parse_params_json():
-    with open("params_json.json", "r") as f:
+def parse_params_json(file_name):
+    with open(file_name, "r") as f:
         params_dict = json.load(f)
-        formatted_dict_json = highlight_json(
-            json.dumps(format_params_dict(params_dict), indent=4)
-        )
+        formatted_dict_json = highlight_json(json.dumps(params_dict, indent=4))
 
     return params_dict, formatted_dict_json
diff --git a/bin/report_modules/templates/params/contents.html b/bin/report_modules/templates/params/contents.html
index 10115c8d..f89d27dd 100644
--- a/bin/report_modules/templates/params/contents.html
+++ b/bin/report_modules/templates/params/contents.html
@@ -4,6 +4,6 @@
             <div class="section-heading">Pipeline Parameters</div>
         </div>
         <div class="section-para-wrapper"><p class="section-para">Only displaying parameters that differ from the pipeline defaults.</p></div>
-        {{ all_stats_dicts['PARAMS_TABLE'] }}
+        {{ all_stats_dicts['PARAMS_SUMMARY_TABLE'] }}
     </div>
 </div>
diff --git a/lib/WorkflowAssemblyqc.groovy b/lib/WorkflowAssemblyqc.groovy
index e5b77980..c410665b 100755
--- a/lib/WorkflowAssemblyqc.groovy
+++ b/lib/WorkflowAssemblyqc.groovy
@@ -49,6 +49,10 @@ class WorkflowAssemblyqc {
     }
 
     public static String jsonifyParams(params) {
+        return JsonOutput.toJson(params).toString()
+    }
+
+    public static String jsonifySummaryParams(params) {
 
         def summary = [:]
         for (group in params.keySet()) {
diff --git a/modules/local/createreport.nf b/modules/local/createreport.nf
index 29ea765c..820f106e 100644
--- a/modules/local/createreport.nf
+++ b/modules/local/createreport.nf
@@ -2,7 +2,7 @@ process CREATEREPORT {
     tag "AssemblyQC"
     label 'process_single'
 
-    // container "docker.io/gallvp/python3npkgs:v0.4"
+    container "docker.io/gallvp/python3npkgs:v0.6"
 
     input:
     path fastavalidator_logs, stageAs: 'fastavalidator_logs/*'
@@ -19,19 +19,30 @@ process CREATEREPORT {
     path circos_outputs, stageAs: 'circos_outputs/*'
     path versions
     val params_json
+    val params_summary_json
 
     output:
     path 'report.html'  , emit: html
     path 'report.json'  , emit: json
-    path "versions.yml" , emit: versions
+    path 'versions.yml' , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     """
-    echo -n '$params_json' > params_json.json
-    assemblyqc.py > report.html
+    echo \\
+        -n \\
+        '$params_json' \\
+        > params_json.json
+
+    echo \\
+        -n \\
+        '$params_summary_json' \\
+        > params_summary_json.json
+
+    assemblyqc.py \\
+        > report.html
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/workflows/assemblyqc.nf b/workflows/assemblyqc.nf
index 198e106a..17ca3f67 100644
--- a/workflows/assemblyqc.nf
+++ b/workflows/assemblyqc.nf
@@ -438,7 +438,8 @@ workflow ASSEMBLYQC {
         ch_hic_html                         .collect().ifEmpty([]),
         ch_synteny_plot                     .collect().ifEmpty([]),
         CUSTOM_DUMPSOFTWAREVERSIONS         .out.yml,
-        Channel.of ( WorkflowAssemblyqc.jsonifyParams ( summary_params ) )
+        Channel.of ( WorkflowAssemblyqc.jsonifyParams ( params ) ),
+        Channel.of ( WorkflowAssemblyqc.jsonifySummaryParams ( summary_params ) )
     )
 }