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tasks/NGScheckMates.wdl
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| 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 0.1 | ||||
| # rename | # rename | ||||
| mv output_all.txt ${sample_id}_output_all.txt | mv output_all.txt ${sample_id}_output_all.txt | ||||
| mv wd.txt ${sample_id}_wd.txt | |||||
| mv output_corr_matrix.txt ${sample_id}_output_corr_matrix.txt | mv output_corr_matrix.txt ${sample_id}_output_corr_matrix.txt | ||||
| mv output_matched.txt ${sample_id}_output_matched.txt | mv output_matched.txt ${sample_id}_output_matched.txt | ||||
| mv r_script.r ${sample_id}_r_script.r | mv r_script.r ${sample_id}_r_script.r | ||||
| } | } | ||||
| output { | output { | ||||
| File all_txt="${sample_id}_output_all.txt" | File all_txt="${sample_id}_output_all.txt" | ||||
| File ncm="${sample_id}_wd.txt" | |||||
| File cor_txt="${sample_id}_output_corr_matrix.txt" | File cor_txt="${sample_id}_output_corr_matrix.txt" | ||||
| File matched_txt="${sample_id}_output_matched.txt" | File matched_txt="${sample_id}_output_matched.txt" | ||||
| File r_script="${sample_id}_r_script.r" | File r_script="${sample_id}_r_script.r" |
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