fix tabix/tabix stub (#9544)

* fix tabix stub

* bump max shards to 16

Author: nvnieuwk

.github/workflows/nf-test.yml

@@ -77,7 +77,7 @@ jobs:
         env:
           NFT_VER: ${{ env.NFT_VER }}
         with:
-          max_shards: 15
+          max_shards: 16
           paths: "${{ join(fromJson(steps.list.outputs.components ), ' ') }}"
 
       - name: debug

modules/nf-core/tabix/tabix/main.nf

@@ -30,7 +30,6 @@ process TABIX_TABIX {
     def args = task.ext.args ?: ''
     def index = args.contains("-C ") || args.contains("--csi") ? "csi" : "tbi"
     """
-    touch ${tab}.tbi
-    touch ${tab}.csi
+    touch ${tab}.${index}
     """
 }

modules/nf-core/tabix/tabix/tests/main.nf.test.snap

@@ -130,10 +130,7 @@
                         {
                             "id": "vcf_csi_stub"
                         },
-                        [
-                            "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                        ]
+                        "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -148,10 +145,7 @@
                         {
                             "id": "vcf_csi_stub"
                         },
-                        [
-                            "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                        ]
+                        "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions_tabix": [
@@ -164,10 +158,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.7"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-11-20T13:47:46.12436"
+        "timestamp": "2025-12-10T14:31:29.90297082"
     },
     "sarscov2_vcf_csi": {
         "content": [

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

@@ -32,10 +32,7 @@
                             "id": "test"
                         },
                         "test.vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
-                        [
-                            "test.vep.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "test.vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                        ]
+                        "test.vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -65,10 +62,7 @@
                             "id": "test"
                         },
                         "test.vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
-                        [
-                            "test.vep.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "test.vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                        ]
+                        "test.vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
@@ -77,9 +71,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-11-28T09:51:42.245769"
+        "timestamp": "2025-12-10T14:35:25.633650675"
     }
 }

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

@@ -53,10 +53,7 @@
                         {
                             "id": "test"
                         },
-                        [
-                            "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                        ]
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "2": [
@@ -68,10 +65,7 @@
                         {
                             "id": "test"
                         },
-                        [
-                            "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                        ]
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "vcf": [
@@ -101,9 +95,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-11-27T16:36:39.797305"
+        "timestamp": "2025-12-10T14:41:23.392663555"
     }
 }