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Refactor GAWK implicit closures #9435

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Refactor GAWK implicit closures #9435

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8 changes: 4 additions & 4 deletions modules/nf-core/gawk/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -23,15 +23,15 @@ process GAWK {
def args = task.ext.args ?: '' // args is used for the main arguments of the tool
def args2 = task.ext.args2 ?: '' // args2 is used to specify a program when no program file has been given
prefix = task.ext.prefix ?: "${meta.id}"
suffix = task.ext.suffix ?: "${input.collect{ it.getExtension()}.get(0)}" // use the first extension of the input files
suffix = task.ext.suffix ?: "${input.collect{ file -> file.getExtension()}.get(0)}" // use the first extension of the input files

program = program_file ? "-f ${program_file}" : "${args2}"
lst_gz = input.findResults{ it.getExtension().endsWith("gz") ? it.toString() : null }
lst_gz = input.findResults{ file -> file.getExtension().endsWith("gz") ? file.toString() : null }
unzip = lst_gz ? "gunzip -q -f ${lst_gz.join(" ")}" : ""
input_cmd = input.collect { it.toString() - ~/\.gz$/ }.join(" ")
input_cmd = input.collect { file -> file.toString() - ~/\.gz$/ }.join(" ")
output_cmd = suffix.endsWith("gz") ? "| gzip > ${prefix}.${suffix}" : "> ${prefix}.${suffix}"
output = disable_redirect_output ? "" : output_cmd
cleanup = lst_gz ? "rm ${lst_gz.collect{ it - ~/\.gz$/ }.join(" ")}" : ""
cleanup = lst_gz ? "rm ${lst_gz.collect{ file -> file - ~/\.gz$/ }.join(" ")}" : ""

input.collect{
assert it.name != "${prefix}.${suffix}" : "Input and output names are the same, set prefix in module configuration to disambiguate!"
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