86 lines
1.8 KiB
Plaintext
Executable File
86 lines
1.8 KiB
Plaintext
Executable File
# msi
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task msi_single {
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String name
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String bed
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String output_dir
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String rmdup_bam
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command <<<
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if [ ! -d ${output_dir}/msi ];then
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mkdir ${output_dir}/msi
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fi
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msisensor2 msi \
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-M /dataseq/jmdna/software/msisensor2/models_hg19_GRCh37 \
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-t ${output_dir}/alignment/${name}.rmdup.bam \
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-e ${bed} \
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-b 10 \
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-o ${output_dir}/msi/${name}.msi.txt
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>>>
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}
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task msi_paired {
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String bed
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String name
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String output_dir
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String tumor_rmdup_bam
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String normal_rmdup_bam
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command <<<
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if [ ! -d ${output_dir}/msi ];then
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mkdir ${output_dir}/msi
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fi
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msisensor2 msi \
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-d /dataseq/jmdna/software/msisensor2/hg19.microsatellites.list \
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-n ${normal_rmdup_bam} \
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-t ${tumor_rmdup_bam} \
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-e ${bed} \
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-b 10 \
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-o ${output_dir}/msi/${name}.msi.txt
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>>>
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}
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workflow call_msi {
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Boolean run=true
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String tumor
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String tumor_rmdup_bam
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String? normal
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String? normal_rmdup_bam
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String bed
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String output_dir
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if (run) {
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# 单样本
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if (!defined(normal)) {
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call msi_single {
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input:
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name=tumor,
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output_dir=output_dir,
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rmdup_bam=tumor_rmdup_bam,
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bed=bed
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}
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}
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# 双样本
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if (defined(normal)) {
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call msi_paired {
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input:
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name=tumor,
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bed=bed,
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output_dir=output_dir,
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tumor_rmdup_bam=tumor_rmdup_bam,
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normal_rmdup_bam=normal_rmdup_bam
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}
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}
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}
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output {
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String msi_txt = "${output_dir}/msi/${tumor}.msi.txt"
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}
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}
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