fix: Improve samtools flagstat stub to generate realistic output (nf-core#9064)

* 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
- Critical for pipelines that parse flagstat files for scale factors
- Enables proper testing of downstream processes in stub workflows

The previous stub created empty files that caused parsing failures
when processes attempted to extract mapped read counts from flagstat
output. This change provides realistic flagstat content that matches
the format of actual samtools flagstat output.

* test: Update samtools flagstat snapshots with current versions

- Regenerate snapshots to match current samtools version (1.22.1)
- Fix versions.yml checksum mismatch
- Ensure tests pass with updated container versions

* test: Update bam_stats_samtools snapshots for improved flagstat stub

- Update subworkflow snapshots to match realistic flagstat content
- Fix stub test failures caused by empty file → realistic content change
- All flagstat checksums updated from d41d8cd98f00b204e9800998ecf8427e to 67394650dbae96d1a4fcc70484822159
- Ensures consistency between module and subworkflow test expectations

* test: Fix samtools flagstat snapshots for CI environment

- Update versions.yml checksums to match CI Docker environment
- Use bdc0bfb2b0542580e7cd65e80d8570bc instead of 108a155f2d4a99f50bf3176904208d27
- Keep realistic flagstat content checksums (67394650dbae96d1a4fcc70484822159 for stub)
- Ensures tests pass in both local and CI environments

* test: Update bam_stats_samtools snapshots with Docker profile

- Regenerate snapshots using Docker containers to match CI environment
- All 6 subworkflow tests pass with updated version checksums
- Ensures consistency between local and CI test environments

Author: edmundmiller

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

@@ -35,7 +35,19 @@ process SAMTOOLS_FLAGSTAT {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.flagstat
+    cat <<-END_FLAGSTAT > ${prefix}.flagstat
+    1000000 + 0 in total (QC-passed reads + QC-failed reads)
+    0 + 0 secondary
+    0 + 0 supplementary
+    0 + 0 duplicates
+    900000 + 0 mapped (90.00% : N/A)
+    1000000 + 0 paired in sequencing
+    500000 + 0 read1
+    500000 + 0 read2
+    800000 + 0 properly paired (80.00% : N/A)
+    850000 + 0 with mate mapped to a different chr
+    50000 + 0 with mate mapped to a different chr (mapQ>=5)
+    END_FLAGSTAT
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/samtools/flagstat/tests/main.nf.test.snap

@@ -8,7 +8,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "1": [
@@ -20,7 +20,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "versions": [
@@ -32,7 +32,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T13:31:17.098789"
+        "timestamp": "2025-09-15T15:02:00.813612"
     },
     "BAM": {
         "content": [
@@ -67,6 +67,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T13:31:12.661288"
+        "timestamp": "2025-09-15T15:01:55.232954"
     }
 }

subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap

@@ -17,7 +17,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "2": [
@@ -40,7 +40,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "idxstats": [
@@ -72,7 +72,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T13:37:48.492968"
+        "timestamp": "2025-09-15T15:20:35.417926"
     },
     "test_bam_stats_samtools_single_end - stub": {
         "content": [
@@ -92,7 +92,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "2": [
@@ -115,7 +115,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "idxstats": [
@@ -147,7 +147,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T13:37:43.4053"
+        "timestamp": "2025-09-15T15:20:25.439222"
     },
     "test_bam_stats_samtools_paired_end_cram - stub": {
         "content": [
@@ -167,7 +167,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "2": [
@@ -190,7 +190,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "idxstats": [
@@ -222,7 +222,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T13:37:53.52248"
+        "timestamp": "2025-09-15T15:20:46.02738"
     },
     "test_bam_stats_samtools_single_end": {
         "content": [
@@ -263,7 +263,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T13:37:27.672053"
+        "timestamp": "2025-09-15T15:20:00.064679"
     },
     "test_bam_stats_samtools_paired_end": {
         "content": [
@@ -304,7 +304,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T13:37:32.985079"
+        "timestamp": "2025-09-15T15:20:08.141202"
     },
     "test_bam_stats_samtools_paired_end_cram": {
         "content": [
@@ -345,6 +345,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T13:37:38.347584"
+        "timestamp": "2025-09-15T15:20:16.06318"
     }
 }