64 lines
1.3 KiB
Plaintext
Executable File
64 lines
1.3 KiB
Plaintext
Executable File
task run_tmb {
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String name
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String file
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String project
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String sample_type
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String output_dir
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command <<<
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if [ ! -d ${output_dir}/tmb ];then
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mkdir ${output_dir}/tmb
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fi
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filter_snpindel.pl \
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${file} \
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${output_dir}/tmb/${name}.tmb.txt \
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${output_dir}/tmb/${name}.tmb.tag.txt \
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${project} \
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${sample_type} \
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tmb
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>>>
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output {
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String tmb_txt = "${output_dir}/tmb/${name}.tmb.txt"
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}
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}
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workflow call_tmb {
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Boolean run=true
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String name
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String file
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String project
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String output_dir
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Boolean umi
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if (run) {
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if (umi) {
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call run_tmb as run_tmb_umi {
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input:
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name=name,
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file=file,
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project=project,
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sample_type='c',
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output_dir=output_dir
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}
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}
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if (!umi) {
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call run_tmb as run_tmb_tissue {
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input:
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name=name,
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file=file,
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project=project,
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sample_type='c',
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output_dir=output_dir
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}
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}
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}
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output {
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String tmb_txt = "${output_dir}/tmb/${name}.tmb.txt"
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}
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} |