--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.4.2/modules/flye/assemble/main.nf	Wed Jul 03 15:16:39 2024 -0400
@@ -0,0 +1,51 @@
+process FLYE_ASSEMBLE {
+    tag "$meta.id"
+    label 'process_medium'
+    // errorStrategy 'ignore'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}flye${params.fs}2.8" : null)
+    conda (params.enable_conda ? "bioconda::flye=2.8.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/flye:2.8.1--py37h8270d21_1' :
+        'quay.io/biocontainers/flye:2.8.1--py37h8270d21_1' }"
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    path "${meta.id}${params.fs}*"
+    tuple val(meta), path("${meta.id}${params.fs}assembly.fasta"), emit: assembly, optional: true
+    path "versions.yml"                                          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    reads_platform=\$( echo "$args" | grep -E -o '(--nano|--pacbio)-(raw|corr|hq|hifi)' )
+    flye \\
+        \$(echo "$args" | sed -e "s/\$reads_platform//") \\
+        -t $task.cpus \\
+        --out-dir "${meta.id}" \\
+        \$reads_platform \\
+        $reads
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        flye: \$( flye --version )
+    END_VERSIONS
+
+    grepver=""
+
+    if [ "${workflow.containerEngine}" != "null" ]; then
+        grepver=\$( grep --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
+    else
+        grepver=\$( echo \$( grep --version 2>&1 ) | sed 's/^.*(GNU grep) //; s/ Copyright.*\$//' )
+    fi
+
+    cat <<-END_VERSIONS >> versions.yml
+        grep: \$grepver
+    END_VERSIONS
+    """
+}
\ No newline at end of file