nf-core_modules/modules/sratools/prefetch/main.nf
2022-05-10 12:16:57 +02:00

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process SRATOOLS_PREFETCH {
tag "$id"
label 'process_low'
conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' :
'quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
input:
tuple val(meta), val(id)
path(ncbi_settings)
output:
tuple val(meta), path(id), emit: sra
path 'versions.yml' , emit: versions
when:
task.ext.when == null || task.ext.when
shell:
args = task.ext.args ?: ''
args2 = task.ext.args2 ?: '5 1 100' // <num retries> <base delay in seconds> <max delay in seconds>
template 'retry_with_backoff.sh'
}