--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.2.0/modules/download_ref_genome/main.nf	Fri May 29 13:32:17 2026 +0000
@@ -0,0 +1,63 @@
+process DOWNLOAD_REF_GENOME {
+    tag "${meta.id}"
+    label "process_pico"
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
+    conda (params.enable_conda ? "conda-forge::python=3.10.4 conda-forge::unzip conda-forge::gzip" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ncbi-datasets-pylib:15.31.1--pyhdfd78af_0' :
+        'quay.io/biocontainers/python:3.10.4' }"
+
+    input:
+        val meta
+
+    output:
+        path "*.fna"       , emit: fasta
+        path "*.gff"       , emit: gff
+        path 'versions.yml', emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args = task.ext.args ?: ''
+        prefix   = task.ext.prefix ?: "${meta.id}"
+        """
+        [ -e /usr/local/ssl/cacert.pem ] && export SSL_CERT_FILE=/usr/local/ssl/cacert.pem
+
+        datasets download genome accession --assembly-version latest --include genome,gff3 ${meta.id}
+
+        unzip ncbi_dataset.zip
+
+        stage_ncbi_dataset_genomes.py -in ncbi_dataset -suffix '_genomic.fna' -out "."
+
+        stage_ncbi_dataset_genomes.py -in ncbi_dataset -suffix '.gff' -out "."
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            datasets: \$( datasets --version | sed 's/datasets version: //g' )
+            python: \$( python --version | sed 's/Python //g' )
+        END_VERSIONS
+
+        zcmd=""
+        zver=""
+
+        if type pigz > /dev/null 2>&1; then
+            zcmd="pigz"
+            zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" )
+        elif type gzip > /dev/null 2>&1; then
+            zcmd="gzip"
+        
+            if [ "${workflow.containerEngine}" != "null" ]; then
+                zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' )
+            else
+                zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" )
+            fi
+        fi
+
+        cat <<-END_VERSIONS >> versions.yml
+            \$zcmd: \$zver
+        END_VERSIONS
+        """
+
+}
\ No newline at end of file