Improving FragPipe

.github/workflows/python-app.yml

@@ -273,8 +273,9 @@ jobs:
         run: pip install .
       - name: Test FragPipe file
         run: |
-          wget -nv -P ./fragpipe https://ftp.pride.ebi.ac.uk/pride/data/archive/2025/08/PXD066146/psm.tsv
-          wget -nv -P ./fragpipe https://ftp.pride.ebi.ac.uk/pride/data/archive/2025/08/PXD066146/ion.tsv
+          wget -nv https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/example-projects/PXD062399.zip
+          mkdir -p ./fragpipe
+          unzip -d ./fragpipe PXD062399.zip
           multiqc --fragpipe-plugin ./fragpipe -o ./results_fragpipe
       - uses: actions/upload-artifact@v4
         if: always()

docs/README.md

@@ -243,7 +243,7 @@ You can find example reports on the [docs page](https://bigbio.github.io/pmultiq
 | ProteoBench | ProteoBench results | [ProteoBench Example](https://pmultiqc.quantms.org/ProteoBench/multiqc_report.html) ([disable_hoverinfo](https://pmultiqc.quantms.org/ProteoBench_disable_hoverinfo/multiqc_report.html)) | [ProteoBench data](https://proteobench.cubimed.rub.de/datasets/d01e87b997b84c985868204b1ed26749902fd7f9/d01e87b997b84c985868204b1ed26749902fd7f9_data.zip) |
 | mzIdentML with mzML | mzIdentML with mzML files | [mzIdentML with mzML Example](https://pmultiqc.quantms.org/PXD053068/multiqc_report.html) ([disable_hoverinfo](https://pmultiqc.quantms.org/PXD053068_disable_hoverinfo/multiqc_report.html)) | [PXD053068 folder](https://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD053068/) |
 | mzIdentML with MGF | mzIdentML with MGF files | [mzIdentML with MGF Example](https://pmultiqc.quantms.org/PXD054720/multiqc_report.html) ([disable_hoverinfo](https://pmultiqc.quantms.org/PXD054720_disable_hoverinfo/multiqc_report.html)) | [PXD054720 folder](https://ftp.pride.ebi.ac.uk/pride/data/archive/2024/08/PXD054720/) |
-| FragPipe | FragPipe results | [FragPipe Example](https://pmultiqc.quantms.org/PXD066146/multiqc_report.html) ([disable_hoverinfo](https://pmultiqc.quantms.org/PXD066146_disable_hoverinfo/multiqc_report.html)) | [psm.tsv](https://ftp.pride.ebi.ac.uk/pride/data/archive/2025/08/PXD066146/psm.tsv) |
+| FragPipe | FragPipe results | [FragPipe Example](https://pmultiqc.quantms.org/PXD062399/multiqc_report.html) ([disable_hoverinfo](https://pmultiqc.quantms.org/PXD062399_disable_hoverinfo/multiqc_report.html)) | [PXD062399.zip](https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/example-projects/PXD062399.zip) |
 
 ## 👥 Contributing
 

docs/config.json

@@ -165,21 +165,19 @@
             "file_type": ["mzid", "disable_hoverinfo"]
         },
         {
-            "accession": "PXD066146",
+            "accession": "PXD062399",
             "urls": [
-                "https://ftp.pride.ebi.ac.uk/pride/data/archive/2025/08/PXD066146/psm.tsv",
-                "https://ftp.pride.ebi.ac.uk/pride/data/archive/2025/08/PXD066146/ion.tsv"
+                "https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/example-projects/PXD062399.zip"
             ],
-            "path": "docs/PXD066146",
+            "path": "docs/PXD062399",
             "file_type": ["fragpipe", ""]
         },
         {
-            "accession": "PXD066146_disable_hoverinfo",
+            "accession": "PXD062399_disable_hoverinfo",
             "urls": [
-                "https://ftp.pride.ebi.ac.uk/pride/data/archive/2025/08/PXD066146/psm.tsv",
-                "https://ftp.pride.ebi.ac.uk/pride/data/archive/2025/08/PXD066146/ion.tsv"
+                "https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/example-projects/PXD062399.zip"
             ],
-            "path": "docs/PXD066146_disable_hoverinfo",
+            "path": "docs/PXD062399_disable_hoverinfo",
             "file_type": ["fragpipe", "disable_hoverinfo"]
         }
     ]

pmultiqc/main.py

@@ -152,4 +152,25 @@ def pmultiqc_plugin_execution_start():
             {"pmultiqc/tsv": {"fn": "*.tsv", "num_lines": 0}},
         )
 
+    # FragPipe workflow file (parameters)
+    if "pmultiqc/workflow" not in config.sp:
+        config.update_dict(
+            config.sp,
+            {"pmultiqc/workflow": {"fn": "*.workflow", "num_lines": 0}},
+        )
+
+    # FragPipe manifest file (experiment design)
+    if "pmultiqc/fp-manifest" not in config.sp:
+        config.update_dict(
+            config.sp,
+            {"pmultiqc/fp-manifest": {"fn": "*.fp-manifest", "num_lines": 0}},
+        )
+
+    # MSFragger params file (search engine parameters)
+    if "pmultiqc/fragger_params" not in config.sp:
+        config.update_dict(
+            config.sp,
+            {"pmultiqc/fragger_params": {"fn": "*.params", "num_lines": 0}},
+        )
+
     config.update({"log_filesize_limit": 200 * pow(1024, 3), "thousandsSep_format": ""})

pmultiqc/modules/common/plots/id.py

@@ -403,7 +403,8 @@ def draw_identification(
     cal_num_table_data=None,
     quantms_missed_cleavages=None,
     quantms_modified=None,
-    msms_identified_rate=None
+    msms_identified_rate=None,
+    draw_peptide_id_count=True,
 ):
 
     if cal_num_table_data and cal_num_table_data.get("sdrf_samples"):
@@ -483,33 +484,34 @@ def build_count(data, value_key, sources):
             """,
     )
 
-    draw_config = {
-        "id": "peptide_id_count",
-        "cpswitch": False,
-        "title": "Peptide ID Count",
-        "tt_decimals": 0,
-        "ylab": "Count",
-        "data_labels": plot_label,
-        "save_data_file": False,
-    }
-
-    bar_html = bargraph.plot(
-        peptide_count,
-        pconfig=draw_config,
-    )
-    bar_html = plot_html_check(bar_html)
+    if draw_peptide_id_count:
+        draw_config = {
+            "id": "peptide_id_count",
+            "cpswitch": False,
+            "title": "Peptide ID Count",
+            "tt_decimals": 0,
+            "ylab": "Count",
+            "data_labels": plot_label,
+            "save_data_file": False,
+        }
 
-    add_sub_section(
-        sub_section=sub_sections,
-        plot=bar_html,
-        order=4,
-        description="""
-            Number of unique (i.e. not counted twice) peptide sequences including modifications per Raw file.
-            """,
-        helptext="""
-            Based on statistics calculated from mzTab, mzIdentML (mzid), DIA-NN report files, or FragPipe psm.tsv.
-            """,
-    )
+        bar_html = bargraph.plot(
+            peptide_count,
+            pconfig=draw_config,
+        )
+        bar_html = plot_html_check(bar_html)
+
+        add_sub_section(
+            sub_section=sub_sections,
+            plot=bar_html,
+            order=4,
+            description="""
+                Number of unique (i.e. not counted twice) peptide sequences including modifications per Raw file.
+                """,
+            helptext="""
+                Based on statistics calculated from mzTab, mzIdentML (mzid), DIA-NN report files, or FragPipe psm.tsv.
+                """,
+        )
 
     if quantms_missed_cleavages:
 
@@ -912,8 +914,9 @@ def draw_modifications(sub_section, modified_data):
     )
 
 
-def draw_oversampling(sub_section, oversampling, oversampling_plot, is_maxquant):
-    if is_maxquant:
+def draw_oversampling(sub_section, oversampling, oversampling_plot, data_type: str):
+
+    if data_type == "maxquant" or data_type == "fragpipe":
         draw_config = {
             "id": "oversampling_distribution",
             "cpswitch": False,
@@ -948,9 +951,15 @@ def draw_oversampling(sub_section, oversampling, oversampling_plot, is_maxquant)
                 Oversampling occurs in low-complexity samples or long LC gradients, as well as undersized dynamic
                 exclusion windows for data independent acquisitions.
                 """
-    if is_maxquant:
+    if data_type == "maxquant":
         helptext += "<p>If DIA-Data: this metric is skipped.</p>"
 
+    if data_type == "fragpipe":
+        helptext += """
+            <p>[FragPipe: combined_ion.tsv] This plot shows the distribution of
+            MS/MS spectral counts per ion/peak for each sample.</p>
+            """
+
     add_sub_section(
         sub_section=sub_section,
         plot=bar_html,