--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.7.0/modules/kma/align/main.nf	Mon Jul 15 10:42:02 2024 -0400
@@ -0,0 +1,73 @@
+process KMA_ALIGN {
+    tag "$meta.id"
+    label 'process_micro'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}kma${params.fs}1.4.4" : null)
+    conda (params.enable_conda ? "conda-forge::libgcc-ng bioconda::kma=1.4.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/kma:1.4.3--h7132678_1':
+        'quay.io/biocontainers/kma:1.4.3--h7132678_1' }"
+
+    input:
+        tuple val(meta), path(reads), path(index)
+
+    output:
+        path "${meta.id}_kma_res"
+        tuple val(meta), path("${meta.id}_kma_res${params.fs}*.res")              , emit: res
+        tuple val(meta), path("${meta.id}_kma_res${params.fs}*.mapstat")          , emit: mapstat, optional: true
+        tuple val(meta), path("${meta.id}_kma_res${params.fs}*.frag.gz")          , emit: frags, optional: true
+        tuple val(meta), path("${meta.id}_kma_res${params.fs}*_template_hits.txt"), emit: hits, optional: true
+        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 reads_in = (meta.single_end ? "-i $reads" : "-ipe ${reads[0]} ${reads[1]}")
+        def db = (meta.kma_t_db ?: "${index}")
+        def db_basename = (db ? "${index.baseName}" : '')
+        def get_hit_accs = (meta.get_kma_hit_accs ? 'true' : 'false')
+        def res_dir = prefix + '_kma_res'
+        reads_in = (params.kmaalign_int ? "-int $reads" : "-i $reads")
+        """
+        mkdir -p $res_dir || exit 1
+        kma \\
+            $args \\
+            -t_db $db${params.fs}$db_basename \\
+            -t $task.cpus \\
+            -o $res_dir${params.fs}$prefix \\
+            $reads_in
+
+        if [ "$get_hit_accs" == "true" ]; then
+            grep -v '^#' $res_dir${params.fs}${prefix}.res | \\
+                grep -E -o 'GC[AF]\\_[0-9]+\\.*[0-9]*' > $res_dir${params.fs}${prefix}_template_hits.txt
+        fi
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            kma: \$( kma -v | sed -e 's%KMA-%%' )
+        END_VERSIONS
+
+        mkdirver=""
+        cutver=""
+        grepver=""
+
+        if [ "${workflow.containerEngine}" != "null" ]; then
+            mkdirver=\$( mkdir --help 2>&1 | sed -e '1!d; s/ (.*\$//' |  cut -f1-2 -d' ' )
+            cutver="\$mkdirver"
+            grepver="\$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/) //;' )
+            grepver=\$( echo \$(grep --version 2>&1) | sed 's/^.*(GNU grep) //; s/ Copyright.*\$//' )
+        fi
+
+        cat <<-END_VERSIONS >> versions.yml
+            mkdir: \$mkdirver
+            cut: \$cutver
+            grep: \$grepver
+        END_VERSIONS
+        """
+}
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