--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/modules/kma/index/main.nf	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,57 @@
+process KMA_INDEX {
+    tag "$meta.id"
+    label 'process_nano'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}kma${params.fs}1.4.4" : null)
+    conda (params.enable_conda ? "conda-forge::libgcc-ng bioconda::kma=1.4.3 conda-forge::coreutils" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/kma:1.4.3--h7132678_1':
+        'quay.io/biocontainers/kma:1.4.3--h7132678_1' }"
+
+    input:
+        tuple val(meta), path(fasta)
+
+    output:
+        tuple val(meta), path("${meta.id}_kma_idx"), emit: idx
+        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}_kma_idx"
+        def add_to_db = (meta.kmaindex_t_db ? "-t_db ${meta.kmaindex_t_db}" : '')
+        """
+        mkdir -p $prefix && cd $prefix || exit 1
+        kma \\
+            index \\
+            $args \\
+            $add_to_db \\
+            -i ../$fasta \\
+            -o $prefix
+        cd .. || exit 1
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            kma: \$( kma -v | sed -e 's%KMA-%%' )
+        END_VERSIONS
+
+        mkdirver=""
+        cutver=""
+
+        if [ "${workflow.containerEngine}" != "null" ]; then
+            mkdirver=\$( mkdir --help 2>&1 | sed -e '1!d; s/ (.*\$//' |  cut -f1-2 -d' ' )
+            cutver="\$mkdirver"
+        else
+            mkdirver=\$( mkdir --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
+            cutver=\$( cut --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
+        fi
+
+        cat <<-END_VERSIONS >> versions.yml
+            mkdir: \$mkdirver
+            cut: \$cutver
+            cd: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
+        END_VERSIONS
+        """
+}
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