fix: Improve samtools flagstat stub to generate realistic output

- Replace empty touch command with proper flagstat format in stub
- Include realistic read counts and mapping statistics
- Ensure stub output matches expected flagstat format for parsing
- Fixes stub workflow tests that depend on flagstat content

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <[email protected]>

Author: edmundmiller

modules.json

@@ -129,7 +129,8 @@
                     "samtools/flagstat": {
                         "branch": "master",
                         "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
-                        "installed_by": ["bam_stats_samtools", "modules"]
+                        "installed_by": ["bam_stats_samtools", "modules"],
+                        "patch": "modules/nf-core/samtools/flagstat/samtools-flagstat.diff"
                     },
                     "samtools/idxstats": {
                         "branch": "master",

modules/nf-core/samtools/flagstat/main.nf

@@ -858,12 +858,12 @@
     },
     "skip_trimming with stub": {
         "content": [
-            137
+            190
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-05T10:08:54.671755"
+        "timestamp": "2025-09-05T10:38:29.093856"
     }
 }