1 changed files with 1 additions and 1 deletions
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tasks/battenberg.wdl
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| cp ${tumor_bam_bai} ./${sample_id}.bam.bai | cp ${tumor_bam_bai} ./${sample_id}.bam.bai | ||||
| cp /opt/battenberg_reference/battenberg_wgs.R ./ | cp /opt/battenberg_reference/battenberg_wgs.R ./ | ||||
| /opt/conda/envs/batternberg/bin/Rscript /battenberg_wgs.R -t ${sample_id} -n ${normal_id} --nb ./${normal_id}.bam --tb ./${sample_id}.bam --cpu 4 --sex female -o ./ | |||||
| /opt/conda/envs/batternberg/bin/Rscript ./battenberg_wgs.R -t ${sample_id} -n ${normal_id} --nb ./${normal_id}.bam --tb ./${sample_id}.bam --cpu 4 --sex female -o ./ | |||||
| mkdir ${sample_id}_chr_png | mkdir ${sample_id}_chr_png | ||||
| cp ${sample_id}_subclones_chr*.png ./${sample_id}_chr_png/ | cp ${sample_id}_subclones_chr*.png ./${sample_id}_chr_png/ | ||||
| tar zcvf ./${sample_id}_chr_png.tgz ./${sample_id}_chr_png/ | tar zcvf ./${sample_id}_chr_png.tgz ./${sample_id}_chr_png/ |
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