73 lines
1.7 KiB
Plaintext
Executable File
73 lines
1.7 KiB
Plaintext
Executable File
# chemo
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task run_chemo {
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String name
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String output_dir
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String probe
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String vcf
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String cancer
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String project
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String bam
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String ref
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command {
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if [ ! -d ${output_dir}/chemo ];then
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mkdir ${output_dir}/chemo
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fi
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chemo.py -d $DATABASE/chemo_database.xlsx -probe ${probe} -n ${name} -v ${vcf} -o ${output_dir}/chemo -c ${cancer} -p ${project} -b ${bam} -r ${ref}
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}
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output {
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String chemo_res = "${output_dir}/chemo/${name}.drug.res.txt"
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}
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}
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workflow call_chemo {
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Boolean run=true
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String name
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String? normal
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String output_dir
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String probe
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String vcf
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String cancer
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String project
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String tumor_rmdup_bam
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String? normal_rmdup_bam
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String ref
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if (run) {
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if (defined(normal)) {
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call run_chemo as run_chemo_normal {
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input:
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name=name,
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output_dir=output_dir,
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probe=probe,
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vcf=vcf,
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cancer=cancer,
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project=project,
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bam=normal_rmdup_bam,
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ref=ref
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}
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}
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if (!defined(normal)) {
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call run_chemo as run_chemo_tumor {
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input:
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name=name,
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output_dir=output_dir,
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probe=probe,
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vcf=vcf,
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cancer=cancer,
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project=project,
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bam=tumor_rmdup_bam,
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ref=ref
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}
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}
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}
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output {
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String chemo_res = "${output_dir}/chemo/${name}.drug.res.txt"
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}
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} |