--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/1.0.0/modules/gather_hits/main.nf	Thu May 28 20:31:42 2026 +0000
@@ -0,0 +1,61 @@
+process GATHER_HITS {
+    tag "$meta.id"
+    label 'process_micro'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}pigz${params.fs}2.7" : null)
+    conda (params.enable_conda ? "conda-forge::pigz=2.6" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pigz:2.3.4' :
+        'quay.io/biocontainers/pigz:2.3.4' }"
+
+    input:
+        tuple val(meta), path(genomes_fasta)
+
+    output:
+        tuple val(meta), path("*_template_hits.txt"), emit: sm_template_hits
+        path "versions.yml"                         , emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args = task.ext.args ?: ''
+        def args2 = task.ext.args2 ?: ''
+
+        // Use input file ending as default
+        prefix   = task.ext.prefix ?: "${meta.id}"
+        command  = genomes_fasta.toString().endsWith('.gz') ? 'zcat' : 'cat'
+        """
+        $command \\
+            $args \\
+            $genomes_fasta | \\
+            grep -F '>' | grep -E -o 'GC[AF]\\_[0-9]+\\.*[0-9]*' > ${prefix}.sm_template_hits.txt
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
+        END_VERSIONS
+        
+        mkdirver=""
+        catver=""
+        zver=""
+        grepver=""
+
+        if [ "${workflow.containerEngine}" != "null" ]; then
+            mkdirver=\$( mkdir --help 2>&1 | sed -e '1!d; s/ (.*\$//' |  cut -f1-2 -d' ' )
+            catver=\$( cat --help 2>&1 | sed -e '1!d; s/ (.*\$//' |  cut -f1-2 -d' ' )
+            zver=\$( zcat --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
+            grepver="\$mkdirver"
+        else
+            catver=\$( cat --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
+            zver=\$( zcat --version 2>&1 | sed '1!d; s/^.*(gzip) //' )
+            grepver=\$( echo \$(grep --version 2>&1) | sed 's/^.*(GNU grep) //; s/ Copyright.*\$//' )
+        fi
+
+        cat <<-END_VERSIONS >> versions.yml
+            cat: \$catver
+            zcat: \$zver
+            grep: \$grepver
+        END_VERSIONS
+        """
+}
\ No newline at end of file