Porechop: No barplots if no data.

Closes #1850

CHANGELOG.md

@@ -6,6 +6,7 @@
 
 - Table code now tolerates lambda function calls with bad data ([#1739](https://github.com/ewels/MultiQC/issues/1739))
 - Beeswarm plot now saves data to `multiqc_data`, same as tables ([#1861](https://github.com/ewels/MultiQC/issues/1861))
+- Don't print DOI in module if it's set to an empty string.
 
 ### New Modules
 
@@ -23,6 +24,9 @@
   - Fix bug that broke the module with paired-end data ([#1845](https://github.com/ewels/MultiQC/issues/1845))
 - **HUMID**
   - Fix bug that prevent HUMID stats files from being parsed ([#1856](https://github.com/ewels/MultiQC/issues/1856))
+- **Porechop**
+  - Don't render bar graphs if no samples had any adapters trimmed ([#1850](https://github.com/ewels/MultiQC/issues/1850))
+  - Added report section listing samples that had no adapters trimmed
 
 ## [MultiQC v1.14](https://github.com/ewels/MultiQC/releases/tag/v1.14) - 2023-01-08
 

multiqc/modules/base_module.py

@@ -63,6 +63,7 @@ def __init__(
         self.doi_link = ""
         if type(self.doi) is str:
             self.doi = [self.doi]
+        self.doi = [i for i in self.doi if i != ""]
         if len(self.doi) > 0:
             doi_links = []
             for doi in self.doi:

multiqc/modules/porechop/porechop.py

@@ -17,7 +17,7 @@ def __init__(self):
             anchor="porechop",
             href="https://github.com/rrwick/Porechop",
             info="a tool for finding and removing adapters from Oxford Nanopore reads.",
-            doi="",
+            # doi="",  # No DOI available
         )
 
         # Find and load reports
@@ -38,9 +38,11 @@ def __init__(self):
         self.write_data_file(self.porechop_data, "porechop")
 
         self.porechop_general_stats()
-        self.start_trim_barplot()
-        self.end_trim_barplot()
-        self.middle_split_barplot()
+        if max(len(v) for v in self.porechop_data.values()) > 1:
+            self.start_trim_barplot()
+            self.end_trim_barplot()
+            self.middle_split_barplot()
+        self.no_adapters_found()
 
     def parse_logs(self, logfile):
         """Parsing Logs. Note: careful of ANSI formatting log"""
@@ -241,3 +243,21 @@ def middle_split_barplot(self):
             description="Shows the number of reads that were split due to adapter being present in middle of read.",
             plot=bargraph.plot(self.porechop_data, cats, config),
         )
+
+    def no_adapters_found(self):
+        """Show any samples that did not have any trimming"""
+        no_adapters = []
+        for s_name in self.porechop_data:
+            if len(self.porechop_data[s_name]) == 1:
+                no_adapters.append(s_name)
+        if len(no_adapters):
+            self.add_section(
+                name="No adapters found",
+                anchor="porechop-noadapters",
+                description="The following samples did not have any adapters found - output reads were unchanged from input reads:",
+                content=f"""
+                    <ul>
+                        <li><code>{'</code></li><li><code>'.join(no_adapters)}</code></li>
+                    </ul>
+                """,
+            )

multiqc/utils/report.py

@@ -460,7 +460,7 @@ def dois_tofile():
     # Collect DOIs
     dois = {"MultiQC": ["10.1093/bioinformatics/btw354"]}
     for mod in modules_output:
-        if mod.doi is not None and mod.doi != []:
+        if mod.doi is not None and mod.doi != "" and mod.doi != []:
             dois[mod.anchor] = mod.doi
     # Write to a file
     fn = "multiqc_citations.{}".format(config.data_format_extensions[config.data_format])