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comparison 0.2.0/modules/download_ref_genome/main.nf @ 14:9e80528263c4

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planemo upload
author kkonganti
date Mon, 15 Jul 2024 17:32:05 -0400
parents a5f31c44f8c9
children 7c0407ebbdf3
comparison
equal deleted inserted replaced
13:1e6a6e88db16 14:9e80528263c4
3 label "process_pico" 3 label "process_pico"
4 4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
6 conda (params.enable_conda ? "conda-forge::python=3.10.4" : null) 6 conda (params.enable_conda ? "conda-forge::python=3.10.4" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/python:3.10.4' : 8 'https://depot.galaxyproject.org/singularity/ncbi-datasets-pylib:15.31.1--pyhdfd78af_0' :
9 'quay.io/biocontainers/python:3.10.4' }" 9 'staphb/ncbi-datasets:15.31.1' }"
10 10
11 input: 11 input:
12 val meta 12 val meta
13 13
14 output: 14 output:
21 21
22 script: 22 script:
23 def args = task.ext.args ?: '' 23 def args = task.ext.args ?: ''
24 prefix = task.ext.prefix ?: "${meta.id}" 24 prefix = task.ext.prefix ?: "${meta.id}"
25 """ 25 """
26 [ -e /usr/local/ssl/cacert.pem ] && export SSL_CERT_FILE=/usr/local/ssl/cacert.pem
27
26 datasets download genome accession --assembly-version latest --include genome,gff3 ${meta.id} 28 datasets download genome accession --assembly-version latest --include genome,gff3 ${meta.id}
27 29
28 unzip ncbi_dataset.zip 30 unzip ncbi_dataset.zip
29 31
30 stage_ncbi_dataset_genomes.py -in ncbi_dataset -suffix '_genomic.fna' -out "." 32 stage_ncbi_dataset_genomes.py -in ncbi_dataset -suffix '_genomic.fna' -out "."