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tasks/NGScheckMates.wdl
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| set -e | set -e | ||||
| nt=$(nproc) | nt=$(nproc) | ||||
| export NCM_HOME=/opt/NGSCheckMate | export NCM_HOME=/opt/NGSCheckMate | ||||
| python /opt/NGSCheckMate/ncm_fastq.py -l ${input_file} -pt /opt/NGSCheckMate/SNP/SNP.pt -O '.' -p $nt -f -s 0.1 | |||||
| python /opt/NGSCheckMate/ncm_fastq.py -l ${input_file} -pt /opt/NGSCheckMate/SNP/SNP.pt -O '.' -p $nt -f -s 0.3 | |||||
| # rename | # rename | ||||
| mv output_all.txt ${sample_id}_output_all.txt | mv output_all.txt ${sample_id}_output_all.txt | ||||
| mv output_corr_matrix.txt ${sample_id}_output_corr_matrix.txt | mv output_corr_matrix.txt ${sample_id}_output_corr_matrix.txt |
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