--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.4.2/modules/spades/assemble/main.nf	Thu Jun 27 14:17:26 2024 -0400
@@ -0,0 +1,47 @@
+process SPADES_ASSEMBLE {
+    tag "$meta.id"
+    label 'process_higher'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}spades${params.fs}3.15.3" : null)
+    conda (params.enable_conda ? 'bioconda::spades=3.15.3' : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/spades:3.15.3--h95f258a_0' :
+        'quay.io/biocontainers/spades:3.15.3--h95f258a_0' }"
+
+    input:
+    tuple val(meta), path(illumina), path(pacbio), path(nanopore)
+
+    output:
+    path "${meta.id}${params.fs}*"
+    tuple val(meta), path("${meta.id}${params.fs}scaffolds.fasta"), emit: assembly, optional: true
+    tuple val(meta), path("${meta.id}${params.fs}spades.log")     , emit: log
+    path  "versions.yml"                                          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def maxmem = task.memory ? "--memory ${task.memory.toGiga()}" : ""
+    def illumina_reads = illumina ? ( meta.single_end ? "-s $illumina" : "-1 ${illumina[0]} -2 ${illumina[1]}" ) : ""
+    def pacbio_reads = !(pacbio.simpleName ==~ 'dummy_file.*') ? "--pacbio $pacbio" : ""
+    def nanopore_reads = !(nanopore.simpleName ==~ 'dummy_file.*') ? "--nanopore $nanopore" : ""
+    def custom_hmms = params.spades_hmm ? "--custom-hmms ${params.spades_hmm}" : ""
+    """
+    spades.py \\
+        $args \\
+        --threads $task.cpus \\
+        $maxmem \\
+        $custom_hmms \\
+        $illumina_reads \\
+        $pacbio_reads \\
+        $nanopore_reads \\
+        -o ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        spades: \$(spades.py --version 2>&1 | sed 's/^.*SPAdes genome assembler v//; s/ .*\$//')
+    END_VERSIONS
+    """
+}
\ No newline at end of file