--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.7.0/modules/sourmash/sig/kmers/main.nf	Mon Jul 15 10:42:02 2024 -0400
@@ -0,0 +1,55 @@
+process SOURMASH_SIG_KMERS {
+    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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/sourmash:4.6.1--hdfd78af_0' :
+        'quay.io/biocontainers/sourmash:4.6.1--hdfd78af_0' }"
+
+    input:
+        tuple val(meta), path(sig_or_seq), path(sequence)
+
+    output:
+        tuple val(meta), path("*.csv")  , emit: signatures, optional: true
+        tuple val(meta), path("*.fasta"), emit: extracted_fasta, optional: true
+        path "versions.yml"             , emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        // required defaults for the tool to run, but can be overridden
+        def args = task.ext.args ?: ''
+        def is_seq = "${sig_or_seq.baseName.findAll(/(?i)\.(fa|fasta|fna)\.{0,1}(gz){0,1}$/).size()}"
+        def save_kmers = (params.sourmashsigkmers_save_kmers ? "--save-kmers ${meta.id}.sm.kmers.csv" : '')
+        def save_seqs = (params.sourmashsigkmers_save_seqs ? "--save-sequences ${meta.id}.sm.seq.fasta" : '')
+        def sketch_mode = (params.sourmashsketch_mode ?: 'dna')
+        def sketch_p = (params.sourmashsketch_p ?: "abund,scaled=1000,k=71")
+        def prefix = task.ext.prefix ?: "${meta.id}"
+        """
+        db_sig="${sig_or_seq}"
+        if [[ $is_seq -ge 1 ]]; then
+            db_sig="${prefix}.db.sig"
+            sourmash sketch \\
+                $sketch_mode \\
+                -p '$sketch_p' \\
+                --output \$db_sig \\
+                $sig_or_seq
+        fi
+
+        sourmash signature kmers \\
+            $args \\
+            $save_kmers \\
+            $save_seqs \\
+            --signatures \$db_sig \\
+            --sequences $sequence 
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            sourmash: \$(echo \$(sourmash --version 2>&1) | sed 's/^sourmash //' )
+            bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
+        END_VERSIONS
+        """
+}
\ No newline at end of file