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37 lines
1.1 KiB
Text
37 lines
1.1 KiB
Text
def MODULE = "bedtools_intersect"
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params.publish_dir = MODULE
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params.publish_results = "default"
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process INTERSECT_BED {
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tag "$input_file_1-$input_file_2"
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publishDir "${params.out_dir}/${params.publish_dir}",
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mode: params.publish_dir_mode,
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saveAs: { filename ->
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if (params.publish_results == "none") null
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else filename }
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container "docker.pkg.github.com/nf-core/$MODULE"
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conda "${moduleDir}/environment.yml"
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input:
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path (input_file_1)
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path (input_file_2)
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val (intersectbed_args)
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output:
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path "${input_file_1.baseName}_i_${input_file_2.baseName}.bed", emit: intersect
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path "*.version.txt", emit: version
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script:
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def params_string = intersectbed_args.collect {
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/-$it.key $it.value/
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} join " "
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"""
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bedtools intersect -a ${input_file_1} -b ${input_file_2} ${params_string} > ${input_file_1.baseName}_i_${input_file_2.baseName}.bed
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bedtools --version | sed -n "s/.*\\(v.*\$\\)/\\1/p" > bedtools.version.txt
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"""
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}
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