63 lines
1.4 KiB
Plaintext
63 lines
1.4 KiB
Plaintext
task run_post {
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String? mutation
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String? fusion
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String? cnv
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String? msi
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String? hereditary
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String? chemo
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String name
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String? normal
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String output_dir
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String cancer
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command <<<
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if [ ! -d ${output_dir}/report ];then
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mkdir ${output_dir}/report
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fi
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indication.pl ${output_dir} ${cancer}
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sample_post.py -s ${normal} -o ${output_dir}
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postprocess.py -n ${name} -s ${normal} -c ${output_dir} -o ${output_dir}/report/${name}.merged_file.xlsx
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>>>
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output {
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String merged = "${output_dir}/report/${name}.merged_file.xlsx"
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}
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}
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workflow call_postprocess {
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Boolean run=true
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String? mutation
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String? fusion
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String? cnv
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String? msi
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String? hereditary
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String? chemo
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String name
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String? normal
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String output_dir
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String cancer
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if (run) {
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call run_post {
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input:
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mutation=mutation,
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fusion=fusion,
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cnv=cnv,
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msi=msi,
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hereditary=hereditary,
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chemo=chemo,
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name=name,
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normal=normal,
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normal=normal,
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output_dir=output_dir,
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cancer=cancer
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}
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}
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output {
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String merged = "${output_dir}/report/${name}.merged_file.xlsx"
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}
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}
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