From 759f2cc0da2fda96610a5d4bd0b8f65dd96a3566 Mon Sep 17 00:00:00 2001
From: vladsaveliev <vladislav.savelyev@populationgenomics.org.au>
Date: Fri, 3 May 2024 21:39:38 +0200
Subject: [PATCH 1/5] Fixes for MultiQC version 1.22

---
 multiqc_ngi/__init__.py               | 2 +-
 multiqc_ngi/multiqc_ngi.py            | 3 ++-
 multiqc_ngi/templates/ngi/header.html | 2 +-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/multiqc_ngi/__init__.py b/multiqc_ngi/__init__.py
index 5a6366f..18d4afa 100644
--- a/multiqc_ngi/__init__.py
+++ b/multiqc_ngi/__init__.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 from importlib.metadata import version
-from multiqc.utils import config
+from multiqc import config
 
 __version__ = version("multiqc_ngi")
 config.multiqc_ngi_version = __version__
diff --git a/multiqc_ngi/multiqc_ngi.py b/multiqc_ngi/multiqc_ngi.py
index 1ddf522..3d9c079 100644
--- a/multiqc_ngi/multiqc_ngi.py
+++ b/multiqc_ngi/multiqc_ngi.py
@@ -18,7 +18,8 @@
 
 __version__ = version("multiqc_ngi")
 
-from multiqc.utils import report, util_functions, config
+from multiqc import report, config
+from multiqc.utils import util_functions
 
 log = logging.getLogger('multiqc')
 
diff --git a/multiqc_ngi/templates/ngi/header.html b/multiqc_ngi/templates/ngi/header.html
index 0291e7d..6bef2b4 100644
--- a/multiqc_ngi/templates/ngi/header.html
+++ b/multiqc_ngi/templates/ngi/header.html
@@ -118,7 +118,7 @@ <h4>JavaScript Disabled</h4>
   &nbsp; <small><em>(6:06)</em></small>
 </div>
 
-{% if report.num_hc_plots > 0 and report.general_stats_html['rows'] | length > config.num_datasets_plot_limit %}
+{% if report.plot_data | length > 0 and report.general_stats_html['rows'] | length > config.num_datasets_plot_limit %}
 <div id="mqc-warning-many-samples" class="alert alert-warning alert-dismissible hidden-print">
   <button type="button" class="close" data-dismiss="alert" aria-label="Close"><span aria-hidden="true">&times;</span></button>
   <span class="glyphicon glyphicon-warning-sign" aria-hidden="true"></span>

From a192584be217a47174e3e8a83f0811306956b5f9 Mon Sep 17 00:00:00 2001
From: vladsaveliev <vladislav.savelyev@populationgenomics.org.au>
Date: Fri, 3 May 2024 21:42:09 +0200
Subject: [PATCH 2/5] Pin MultiQC

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 26461c8..2aa9862 100755
--- a/setup.py
+++ b/setup.py
@@ -30,7 +30,7 @@
         'simplejson',
         'pyyaml',
         'requests',
-        'multiqc'
+        'multiqc>=1.22.dev0'
     ],
     entry_points = {
         'multiqc.templates.v1': [

From 1ace4a135f313c9ed7f338da91f0a09a3d889323 Mon Sep 17 00:00:00 2001
From: vladsaveliev <vladislav.savelyev@populationgenomics.org.au>
Date: Mon, 6 May 2024 15:56:34 +0200
Subject: [PATCH 3/5] write_data_file is a method of report

---
 multiqc_ngi/multiqc_ngi.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/multiqc_ngi/multiqc_ngi.py b/multiqc_ngi/multiqc_ngi.py
index 3d9c079..2b0315e 100644
--- a/multiqc_ngi/multiqc_ngi.py
+++ b/multiqc_ngi/multiqc_ngi.py
@@ -322,7 +322,7 @@ def general_stats_sample_meta(self):
             log.info('Found {} samples in StatusDB'.format(len(meta)))
 
             # Write to file
-            util_functions.write_data_file(meta, 'ngi_meta')
+            report.write_data_file(meta, 'ngi_meta')
 
             # Add to General Stats table
             gsdata = dict()

From 1147bc0d73ccb019c9209287f28567cbaf9161e6 Mon Sep 17 00:00:00 2001
From: vladsaveliev <vladislav.savelyev@populationgenomics.org.au>
Date: Mon, 13 May 2024 10:24:03 +0200
Subject: [PATCH 4/5] modules_ouptut -> modules

---
 multiqc_ngi/multiqc_ngi.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/multiqc_ngi/multiqc_ngi.py b/multiqc_ngi/multiqc_ngi.py
index 2b0315e..a5e2cee 100644
--- a/multiqc_ngi/multiqc_ngi.py
+++ b/multiqc_ngi/multiqc_ngi.py
@@ -296,7 +296,7 @@ def get_ngi_samples_metadata(self, pid, s_names=None):
     def fastqscreen_genome(self):
         """Add the Refrence genome from statusdb to fastq_screen html"""
         if report.ngi.get('reference_genome') is not None:
-            for m in report.modules_output:
+            for m in report.modules:
                 if m.anchor  == 'fastq_screen':
                     genome=report.ngi['reference_genome']
                     nice_names = {

From 07d0f4a046cbc14f1cfaeea0c0f655529e099231 Mon Sep 17 00:00:00 2001
From: vladsaveliev <vladislav.savelyev@populationgenomics.org.au>
Date: Fri, 17 May 2024 06:54:12 -0400
Subject: [PATCH 5/5] Fix for analysis_dir as Path

---
 multiqc_ngi/multiqc_ngi.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/multiqc_ngi/multiqc_ngi.py b/multiqc_ngi/multiqc_ngi.py
index a5e2cee..efd3a56 100644
--- a/multiqc_ngi/multiqc_ngi.py
+++ b/multiqc_ngi/multiqc_ngi.py
@@ -234,7 +234,7 @@ def get_ngi_project_metadata(self, pid):
 
         config.title = '{}: {}'.format(pid, p_summary['project_name'])
         config.project_name = p_summary['project_name']
-        if config.analysis_dir and ('qc_ngi' in config.analysis_dir[0] or 'qc_ngi' in os.listdir()):
+        if config.analysis_dir and ('qc_ngi' in str(config.analysis_dir[0]) or 'qc_ngi' in os.listdir()):
             infix = 'qc'
         else:
             infix = 'pipeline'