1 changed files with 10 additions and 5 deletions
+ 10
- 5
tasks/CNVkit.wdl
View File
| #WES | #WES | ||||
| if [ ${bed_file} ]; then | if [ ${bed_file} ]; then | ||||
| echo "WES" | |||||
| if [ ${normal_bam} ]; then | if [ ${normal_bam} ]; then | ||||
| echo "WES with normal" | |||||
| /root/miniconda2/bin/cnvkit.py target ${bed_file} --annotate ${ref_flat} --split --short-names -o my_baits.bed | /root/miniconda2/bin/cnvkit.py target ${bed_file} --annotate ${ref_flat} --split --short-names -o my_baits.bed | ||||
| /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \ | /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \ | ||||
| --normal ${normal_bam} \ | --normal ${normal_bam} \ | ||||
| --drop-low-coverage \ | --drop-low-coverage \ | ||||
| --output-dir ${sample}.reference.cnn | --output-dir ${sample}.reference.cnn | ||||
| else | else | ||||
| echo "WES no normal" | |||||
| /root/miniconda2/bin/cnvkit.py access ${ref_dir} -o access.bed | /root/miniconda2/bin/cnvkit.py access ${ref_dir} -o access.bed | ||||
| # Prepare the target bed | # Prepare the target bed | ||||
| /root/miniconda2/bin/cnvkit.py target ${bed_file} --annotate ${ref_flat} --split --short-names -o my_baits.bed | /root/miniconda2/bin/cnvkit.py target ${bed_file} --annotate ${ref_flat} --split --short-names -o my_baits.bed | ||||
| /root/miniconda2/bin/cnvkit.py autobin ${tumor_bam} -t my_baits.bed -g access.bed | /root/miniconda2/bin/cnvkit.py autobin ${tumor_bam} -t my_baits.bed -g access.bed | ||||
| /root/miniconda2/bin/cnvkit.py coverage ${tumor_bam} ${sample}.target.bed -o ${sample}.T.targetcoverage.cnn | |||||
| /root/miniconda2/bin/cnvkit.py coverage ${tumor_bam} ${sample}.antitarget.bed -o ${sample}.T.antitargetcoverage.cnn | |||||
| /root/miniconda2/bin/cnvkit.py coverage ${tumor_bam} my_baits.target.bed -o ${sample}.T.targetcoverage.cnn | |||||
| /root/miniconda2/bin/cnvkit.py coverage ${tumor_bam} my_baits.antitarget.bed -o ${sample}.T.antitargetcoverage.cnn | |||||
| /root/miniconda2/bin/cnvkit.py reference -o ${sample}.reference.cnn/reference.cnn -f ${ref_dir} -t ${sample}.target.bed -a ${sample}.antitarget.bed | |||||
| /root/miniconda2/bin/cnvkit.py reference -o ${sample}.reference.cnn/reference.cnn -f ${ref_dir} -t my_baits.target.bed -a my_baits.antitarget.bed | |||||
| fi | fi | ||||
| #WGS | #WGS | ||||
| else | else | ||||
| if [ ${normal_bam} ]; then | |||||
| echo "WGS" | |||||
| if [ ${normal_bam} ]; then | |||||
| echo "WGS with normal" | |||||
| /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \ | /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \ | ||||
| --normal ${normal_bam} \ | --normal ${normal_bam} \ | ||||
| --method wgs \ | --method wgs \ | ||||
| --drop-low-coverage \ | --drop-low-coverage \ | ||||
| --output-dir ${sample}.reference.cnn | --output-dir ${sample}.reference.cnn | ||||
| else | else | ||||
| echo "WGS no normal" | |||||
| /root/miniconda2/bin/cnvkit.py access ${ref_dir} -o access.bed | /root/miniconda2/bin/cnvkit.py access ${ref_dir} -o access.bed | ||||
| # Prepare the target bed | # Prepare the target bed | ||||
| #/root/miniconda2/bin/cnvkit.py --annotate ${ref_flat} --split --short-names -o my_baits.bed | #/root/miniconda2/bin/cnvkit.py --annotate ${ref_flat} --split --short-names -o my_baits.bed |
Loading…