nf-cmgg · nvnieuwk · Jun 24, 2025 · May 21, 2025 · May 26, 2025 · May 26, 2025
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -37,3 +37,9 @@ mosdepth_config:
     - "HLA*"
     - "chrM"
     - "chrEBV"
+
+custom_data:
+  msisensorpro_summary:
+    pattern: "*_unstable"  # or your actual filename pattern
+    section_name: "MSIsensorPro Summary"
+    description: "Summary of MSI sites per sample"
diff --git a/main.nf b/main.nf
@@ -166,6 +166,7 @@ workflow {
         params.outdir,
         GlobalVariables.pedFiles,
         params.elsites,
+        params.msi_baseline,
 
         // Boolean inputs
         params.dragstr,

diff --git a/modules.json b/modules.json
@@ -129,6 +129,11 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/mosdepth/mosdepth.diff"
                     },
+                    "msisensorpro/pro": {
+                        "branch": "master",
+                        "git_sha": "fafa7b3a577412b6bde309170408da4cb911f04b",
+                        "installed_by": ["modules"]
+                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c",

diff --git a/modules/nf-core/msisensorpro/pro/environment.yml b/modules/nf-core/msisensorpro/pro/environment.yml
diff --git a/modules/nf-core/msisensorpro/pro/main.nf b/modules/nf-core/msisensorpro/pro/main.nf
diff --git a/modules/nf-core/msisensorpro/pro/meta.yml b/modules/nf-core/msisensorpro/pro/meta.yml
diff --git a/modules/nf-core/msisensorpro/pro/tests/main.nf.test b/modules/nf-core/msisensorpro/pro/tests/main.nf.test