--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/modules/sourmash/sketch/main.nf	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,48 @@
+process SOURMASH_SKETCH {
+    tag "$meta.id"
+    label 'process_micro'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}sourmash${params.fs}4.6.1" : null)
+    conda (params.enable_conda ? "conda-forge::python bioconda::sourmash=4.6.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/sourmash:4.6.1--hdfd78af_0':
+        'quay.io/biocontainers/sourmash:4.6.1--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(sequence), path(database)
+
+    output:
+    tuple val(meta), path("*.query.sig"), path("*.db.sig"), emit: signatures
+    path "versions.yml"                                   , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // required defaults for the tool to run, but can be overridden
+    def args = task.ext.args ?: ''
+    def args_query 
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    sourmash sketch \\
+        ${args.toString().replace('--singleton', '')} \\
+        --output "${prefix}.query.pre" \\
+        $sequence
+
+    sourmash signature rename \\
+        --${args.toString().replaceAll(/\s+\-p.*/, '')} \\
+        -o "${prefix}.query.sig" \\
+        "${prefix}.query.pre" \\
+        ${prefix} 
+
+    sourmash sketch \\
+        $args \\
+        --output "${prefix}.db.sig" \\
+        $database
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sourmash: \$(echo \$(sourmash --version 2>&1) | sed 's/^sourmash //' )
+    END_VERSIONS
+    """
+}
\ No newline at end of file