Fix: PoolSNP: Update input tuple; cleanup stub (#8218)

* Update input tuple; cleanup stub

* Update meta.yml for poolsnp

Author: abhilesh

modules/nf-core/poolsnp/main.nf

@@ -10,7 +10,7 @@ process POOLSNP {
     input:
     tuple val(meta) , path(mpileup)
     tuple val(meta2), path(reference)
-    tuple val(meta) , val(max_cov), path(max_cov_file)
+    tuple val(meta3), val(max_cov), path(max_cov_file)
 
     output:
     tuple val(meta), path("*.vcf.gz")  , emit: vcf
@@ -44,7 +44,6 @@ process POOLSNP {
     """
 
     stub:
-    def args   = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 

modules/nf-core/poolsnp/meta.yml

@@ -40,7 +40,7 @@ input:
           Reference genome in FASTA format.
           May NOT contain any special characters such as "/|,:"
         pattern: "*.{fasta,fa}"
-  - - meta:
+  - - meta3:
         type: map
         description: |
           Groovy Map containing sample information.

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

@@ -8,17 +8,18 @@
             [
                 [
                     {
-                        "id": "test"
+                        "id": "test",
+                        "single_end": false
                     },
                     "test_cov-0.7.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ]
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-08-16T15:51:10.298893"
+        "timestamp": "2025-04-05T11:57:13.661565"
     },
     "sarscov2 - mpileup - max_cov_file - stub": {
         "content": [
@@ -42,17 +43,18 @@
             [
                 [
                     {
-                        "id": "test"
+                        "id": "test",
+                        "single_end": false
                     },
                     "test-cov-0.7.txt:md5,ccbb119522c09daa976a9015ba999329"
                 ]
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-08-16T15:30:50.011"
+        "timestamp": "2025-04-05T11:56:50.034677"
     },
     "sarscov2 - mpileup - max_cov_file": {
         "content": [