--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.1.0/modules/mash/sketch/main.nf	Mon Nov 27 12:37:44 2023 -0500
@@ -0,0 +1,44 @@
+process MASH_SKETCH {
+    tag "${meta.id}"
+    label 'process_micro'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}mash${params.fs}2.3" : null)
+    conda (params.enable_conda ? "conda-forge::capnproto conda-forge::gsl bioconda::mash=2.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1':
+        'quay.io/biocontainers/mash:2.3--he348c14_1' }"
+
+    input:
+        tuple val(meta), path(query)
+
+    output:
+        tuple val(meta), path("*.msh")               , emit: sketch
+        tuple val(meta), path("*_mash_sketch.status"), emit: stats
+        path "versions.yml"                          , emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args = task.ext.args ?: ''
+        def prefix = task.ext.prefix ?: "${meta.id}"
+        def queries = (query ? query.collect().join('\\n') : null)
+        sleep(Math.round(params.genomes_chunk.toInteger()) as int * 100)
+        """
+        echo -e "$queries" > sketch_these.txt
+
+        mash \\
+            sketch \\
+            -p $task.cpus \\
+            -o "msh.${task.index}.k${params.mashsketch_k}.${params.mashsketch_s}h.${prefix}" \\
+            $args \\
+            -l sketch_these.txt \\
+            2> ${prefix}_${task.index}_mash_sketch.status
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            mash: \$( mash --version )
+            bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
+        END_VERSIONS
+        """
+}
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