99 lines
1.9 KiB
Plaintext
Executable File
99 lines
1.9 KiB
Plaintext
Executable File
# tmb
|
|
|
|
task run_tmb {
|
|
String name
|
|
String file
|
|
String project
|
|
String sample_type
|
|
String output_dir
|
|
|
|
command {
|
|
if [ ! -d ${output_dir}/tmb ];then
|
|
mkdir ${output_dir}/tmb
|
|
fi
|
|
filter_snpindel.pl \
|
|
${file} \
|
|
${output_dir}/tmb/${name}.tmb.txt \
|
|
${output_dir}/tmb/${name}.tmb.tag.txt \
|
|
${project} \
|
|
${sample_type} \
|
|
tmb
|
|
|
|
}
|
|
|
|
output {
|
|
String tmb_txt = "${output_dir}/tmb/${name}.tmb.txt"
|
|
}
|
|
}
|
|
|
|
task run_tmb_umi {
|
|
String name
|
|
String file
|
|
String project
|
|
String sample_type
|
|
String output_dir
|
|
String tumor_rmdup_bam
|
|
|
|
command {
|
|
if [ ! -d ${output_dir}/tmb ];then
|
|
mkdir ${output_dir}/tmb
|
|
fi
|
|
filter_snpindel.pl \
|
|
${file} \
|
|
${output_dir}/tmb/${name}.tmb.pre.txt \
|
|
${output_dir}/tmb/${name}.tmb.tag.txt \
|
|
${project} \
|
|
${sample_type} \
|
|
tmb
|
|
|
|
correct_umi_overlap_reads.py ${output_dir}/tmb/${name}.tmb.pre.txt ${tumor_rmdup_bam} ${output_dir}/tmb/${name}.tmb.txt
|
|
|
|
|
|
}
|
|
|
|
output {
|
|
String tmb_txt = "${output_dir}/tmb/${name}.tmb.txt"
|
|
}
|
|
}
|
|
|
|
workflow call_tmb {
|
|
|
|
Boolean run=true
|
|
|
|
String name
|
|
String file
|
|
String project
|
|
String output_dir
|
|
Boolean umi
|
|
String tumor_rmdup_bam
|
|
|
|
if (run) {
|
|
if (umi) {
|
|
call run_tmb_umi {
|
|
input:
|
|
name=name,
|
|
file=file,
|
|
project=project,
|
|
sample_type='c',
|
|
output_dir=output_dir,
|
|
tumor_rmdup_bam=tumor_rmdup_bam
|
|
}
|
|
}
|
|
if (!umi) {
|
|
call run_tmb {
|
|
input:
|
|
name=name,
|
|
file=file,
|
|
project=project,
|
|
sample_type='t',
|
|
output_dir=output_dir
|
|
}
|
|
}
|
|
|
|
|
|
}
|
|
|
|
output {
|
|
String tmb_txt = "${output_dir}/tmb/${name}.tmb.txt"
|
|
}
|
|
} |