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comparison microrunqc.xml @ 21:5083f8406e34 draft

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author estrain
date Fri, 19 Jan 2024 11:47:29 +0000
parents b07d5fec5942
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20:9c5e62562c87 21:5083f8406e34
103 --minscore $options.minscore 103 --minscore $options.minscore
104 #end if 104 #end if
105 #end if 105 #end if
106 ${outname}.fasta > ${outname}.mlst_raw.tsv; 106 ${outname}.fasta > ${outname}.mlst_raw.tsv;
107 107
108 perl $__tool_directory__/mlstAddFields.pl ${outname}.mlst_raw.tsv > ${outname}.mlst.tsv; 108 python $__tool_directory__/mlstAddFields.py ${outname}.mlst_raw.tsv $mlst_databases.fields.path/pubmlst > ${outname}.mlst.tsv;
109 109
110 python $__tool_directory__/run_fastq_scan.py --fastq ${bwalist} --out fq_out.tab --type ${fqscan}; 110 python $__tool_directory__/run_fastq_scan.py --fastq ${bwalist} --out fq_out.tab --type ${fqscan};
111 111
112 python $__tool_directory__/sum_mlst.py --fasta ${outname}.fasta --mlst ${outname}.mlst.tsv --med insert.median --fqscan fq_out.tab --out sum_qc.txt 112 python $__tool_directory__/sum_mlst.py --fasta ${outname}.fasta --mlst ${outname}.mlst.tsv --med insert.median --fqscan fq_out.tab --out sum_qc.txt
113 113