--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/1.0.0/modules/medaka/consensus/main.nf	Thu May 28 20:41:10 2026 +0000
@@ -0,0 +1,36 @@
+process MEDAKA_CONSENSUS {
+    tag "$meta.id"
+    label 'process_low'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}medaka${params.fs}1.11.2" : null)
+    conda (params.enable_conda ? "bioconda::medaka=1.11.2 conda-forge::python" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/medaka:1.11.2--py310h87e71ce_0' :
+        'quay.io/biocontainers/medaka:1.11.2--py310h87e71ce_0' }"
+
+    input:
+        tuple val(meta), path(bam), path(bai)
+
+    output:
+        tuple val(meta), path("*.hdr"), emit: hdr
+        path "versions.yml"           , emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args = task.ext.args ?: ''
+        def prefix = task.ext.prefix ?: "${meta.id}"
+        """
+        medaka consensus \\
+            --threads $task.cpus \\
+            $args \\
+            $bam \\
+            ${prefix}.medaka.hdr
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            medaka: \$( medaka --version 2> /dev/null | sed 's/medaka //g' )
+        END_VERSIONS
+        """
+}
\ No newline at end of file