Mercurial > repos > galaxytrakr > hfp_cronology_awsbatch

comparison 0.2.0/modules/download_ref_genome/main.nf @ 0:9e8b1c747a6a draft default tip

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planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:32:17 +0000
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-1:000000000000 0:9e8b1c747a6a
1 process DOWNLOAD_REF_GENOME {
2 tag "${meta.id}"
3 label "process_pico"
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
6 conda (params.enable_conda ? "conda-forge::python=3.10.4 conda-forge::unzip conda-forge::gzip" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/ncbi-datasets-pylib:15.31.1--pyhdfd78af_0' :
9 'quay.io/biocontainers/python:3.10.4' }"
10
11 input:
12 val meta
13
14 output:
15 path "*.fna" , emit: fasta
16 path "*.gff" , emit: gff
17 path 'versions.yml', emit: versions
18
19 when:
20 task.ext.when == null || task.ext.when
21
22 script:
23 def args = task.ext.args ?: ''
24 prefix = task.ext.prefix ?: "${meta.id}"
25 """
26 [ -e /usr/local/ssl/cacert.pem ] && export SSL_CERT_FILE=/usr/local/ssl/cacert.pem
27
28 datasets download genome accession --assembly-version latest --include genome,gff3 ${meta.id}
29
30 unzip ncbi_dataset.zip
31
32 stage_ncbi_dataset_genomes.py -in ncbi_dataset -suffix '_genomic.fna' -out "."
33
34 stage_ncbi_dataset_genomes.py -in ncbi_dataset -suffix '.gff' -out "."
35
36 cat <<-END_VERSIONS > versions.yml
37 "${task.process}":
38 datasets: \$( datasets --version | sed 's/datasets version: //g' )
39 python: \$( python --version | sed 's/Python //g' )
40 END_VERSIONS
41
42 zcmd=""
43 zver=""
44
45 if type pigz > /dev/null 2>&1; then
46 zcmd="pigz"
47 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" )
48 elif type gzip > /dev/null 2>&1; then
49 zcmd="gzip"
50
51 if [ "${workflow.containerEngine}" != "null" ]; then
52 zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' )
53 else
54 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" )
55 fi
56 fi
57
58 cat <<-END_VERSIONS >> versions.yml
59 \$zcmd: \$zver
60 END_VERSIONS
61 """
62
63 }