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prototype.nf
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prototype.nf
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#!/usr/bin/env nextflow
// attach dropbox url to the name of prototype
switch( params.proto ) {
case "prototype-001":
url = 'https://www.dropbox.com/sh/g1daajcl8o1mem1/AAB3zZjaQQK5eAOKT43U8zeZa?dl=0'
break
default:
error "Please enter a valid prototype image name"
}
// create channel from prototype image name
nm = Channel.from( params.proto )
// download data from dropbox
process downloadPrototype {
// export data to prototype folder
publishDir "${params.out}/${params.proto}", mode: 'copy'
input:
val i from nm
output:
path '**' into test
shell:
'''
curl "!{url}" -o input.zip -J -L -k
'''
}
// unzip input folder from dropbox
process unzipInput {
// unzip input folder to get contents for MIAAIM pipeline
publishDir "${params.out}/${params.proto}", mode: 'copy'
input:
path i from test
output:
file '*' into out
shell:
'''
bsdtar -xf "!{i}" && rm "!{i}"
'''
}