1 changed files with 7 additions and 2 deletions
+ 7
- 2
tasks/CNVkit.wdl
View File
| @@ -31,7 +31,9 @@ task cnvkit{ | |||
| #WES | |||
| if [ ${bed_file} ]; then | |||
| echo "WES" | |||
| 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 batch ${tumor_bam} \ | |||
| --normal ${normal_bam} \ | |||
| @@ -41,6 +43,7 @@ task cnvkit{ | |||
| --drop-low-coverage \ | |||
| --output-dir ${sample}.reference.cnn | |||
| else | |||
| echo "WES no normal" | |||
| /root/miniconda2/bin/cnvkit.py access ${ref_dir} -o access.bed | |||
| # Prepare the target bed | |||
| /root/miniconda2/bin/cnvkit.py target ${bed_file} --annotate ${ref_flat} --split --short-names -o my_baits.bed | |||
| @@ -55,8 +58,9 @@ task cnvkit{ | |||
| #WGS | |||
| else: | |||
| if [ ${normal_bam} ]; then | |||
| echo "WGS" | |||
| if [ ${normal_bam} ]; then | |||
| echo "WGS with normal" | |||
| /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \ | |||
| --normal ${normal_bam} \ | |||
| --method wgs \ | |||
| @@ -65,6 +69,7 @@ task cnvkit{ | |||
| --drop-low-coverage \ | |||
| --output-dir ${sample}.reference.cnn | |||
| else | |||
| echo "WGS no normal" | |||
| /root/miniconda2/bin/cnvkit.py access ${ref_dir} -o access.bed | |||
| # Prepare the target bed | |||
| #/root/miniconda2/bin/cnvkit.py --annotate ${ref_flat} --split --short-names -o my_baits.bed | |||
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