Merge pull request #102 from yueqixuan/main

Add mzid plugin

.github/workflows/python-app.yml

@@ -15,9 +15,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: 3.9
     - name: Install dependencies
@@ -41,7 +41,7 @@ jobs:
         unzip -d ./lfq lfq.zip
         python setup.py install
         multiqc -f ./lfq --config ./lfq/multiqc_config.yml -o ./results_lfq
-    - uses: actions/upload-artifact@v1
+    - uses: actions/upload-artifact@v4
       if: always()
       name: Upload results
       with:
@@ -53,7 +53,7 @@ jobs:
         unzip -d ./tmt tmt-replicates.zip
         python setup.py install
         multiqc -f ./tmt --config ./tmt/multiqc_config.yml -o ./results_tmt
-    - uses: actions/upload-artifact@v1
+    - uses: actions/upload-artifact@v4
       if: always()
       name: Upload results
       with:
@@ -65,7 +65,7 @@ jobs:
         unzip -d ./dia dia.zip
         python setup.py install
         multiqc -f ./dia --config  ./dia/multiqc_config.yml -o ./results_dia
-    - uses: actions/upload-artifact@v1
+    - uses: actions/upload-artifact@v4
       if: always()
       name: Upload results
       with:

.github/workflows/python-package.yml

@@ -19,9 +19,9 @@ jobs:
         python-version: [3.8, 3.9, 3.11]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

.github/workflows/python-publish.yml

@@ -21,9 +21,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
     - name: Install dependencies

README.md

@@ -33,6 +33,7 @@ example: ```multiqc resources/LFQ -o ./```
 - --quantification_method: The quantification method for LFQ experiment (default: `feature_intensity`)
 - --disable_table: Disable protein/peptide table plots for large dataset
 - --ignored_idxml: ignored idxml files for faster running
+- --mzid_plugin: Generate reports based on mzid and mzML/mgf
 
 An example report can be found in [multiqc_report.html](http://bigbio.xyz/pmultiqc/shared-peptides-star-align-stricter-pep-protein-FDR/multiqc_report.html)
 

pmultiqc/cli.py

@@ -35,3 +35,4 @@ def print_version(ctx, params, value):
                             help='Prefix (default) or suffix')
 disable_plugin = click.option('--disable_plugin', 'disable_plugin', is_flag=True,
                             help="Disable the pmultiqc plugin on this run")
+mzid_plugin = click.option('--mzid_plugin', 'mzid_plugin', is_flag=True, help="Extract mzIdentML")

pmultiqc/main.py

@@ -43,6 +43,12 @@ def pmultiqc_plugin_execution_start():
     if 'quantms/mzML' not in config.sp:
         config.update_dict(config.sp, {'quantms/mzML': {'fn': '*.mzML', 'num_lines': 0}})
 
+    if 'quantms/mgf' not in config.sp:
+        config.update_dict(config.sp, {'quantms/mgf': {'fn': '*.mgf', 'num_lines': 0}})
+
+    if 'quantms/mzid' not in config.sp:
+        config.update_dict(config.sp, {'quantms/mzid': {'fn': '*.mzid', 'num_lines': 0}})
+
     if 'quantms/ms_info' not in config.sp:
         config.update_dict(config.sp, {'quantms/ms_info': {'fn': '*_ms_info.parquet', 'num_lines': 0}})