Allow gzipped inputs to modkit/bedmethyltobigwig

modules/nf-core/modkit/bedmethyltobigwig/main.nf

@@ -20,16 +20,18 @@ process MODKIT_BEDMETHYLTOBIGWIG {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def mods = modcodes instanceof List ? modcodes.join(',') : modcodes
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    def mods      = modcodes instanceof List ? modcodes.join(',') : modcodes
+    def input_cmd = bedmethyl.getName().endsWith('.gz') ? "gzip -cd" : "cat"
     """
-    modkit bedmethyl tobigwig \\
+    $input_cmd $bedmethyl |\\
+        modkit bedmethyl tobigwig \\
         $args \\
         --nthreads $task.cpus \\
         --sizes $chromsizes \\
         --mod-codes $mods \\
-        $bedmethyl \\
+        - \\
         ${prefix}.bw
 
     cat <<-END_VERSIONS > versions.yml

modules/nf-core/modkit/bedmethyltobigwig/meta.yml

@@ -23,7 +23,7 @@ input:
     - bedmethyl:
         type: file
         description: bedMethyl file
-        pattern: "*.{bed}"
+        pattern: "*.{bed,bed.gz}"
         ontologies:
           - edam: "http://edamontology.org/format_3003" # BED
   - - meta2:

modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test

@@ -60,12 +60,12 @@ nextflow_process {
         }
     }
 
-    test("homo sapiens - bedmethyl, fai, string") {
+    test("homo sapiens - compressed bedmethyl, fai, string") {
 
         when {
             process {
                 """
-                input[0] = TABIX_BGZIP.out.output
+                input[0] = MODKIT_PILEUP.out.bedgz
                 input[1] = [
                     [ id : 'hg38' ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)

modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap

@@ -65,7 +65,7 @@
         },
         "timestamp": "2025-12-11T14:17:52.811754475"
     },
-    "homo sapiens - bedmethyl, fai, string": {
+    "homo sapiens - compressed bedmethyl, fai, string": {
         "content": [
             {
                 "0": [
@@ -94,8 +94,8 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-12-11T14:18:02.079953932"
+        "timestamp": "2025-12-19T10:25:49.934420699"
     }
 }