Commit d2f17c80 authored by peguerin's avatar peguerin
Browse files

fix demultiplex

parent bc764c4f
......@@ -23,7 +23,7 @@ rule demultiplexing:
cat ../results/02_assembly/{params.dmulti[run]}.fastq ../02_assembly/{params.dmulti[run]}_rev.fastq | \
cutadapt --discard-untrimmed -m {params.minLen} -g {params.dmulti[barcode5]} -O {params.dmulti[lenBarcode5]} - | \
cutadapt --discard-untrimmed -m {params.minLen} -g ^{params.dmulti[primer5]} -O {params.dmulti[min_f]} - | \
cutadapt --discard-untrimmed -m {params.minLen} -a {params.dmulti[barcode3]} -O {params.dmulti[lenBarcode3]} - {log} | \
cutadapt --discard-untrimmed -m {params.minLen} -a {params.dmulti[barcode3]} -O {params.dmulti[lenBarcode3]} - | \
cutadapt --discard-untrimmed -m {params.minLen} -a {params.dmulti[primer3]}$ -O {params.dmulti[min_r]} - | \
cutadapt -M {params.maxLen} - 2> {log} > {output}
'''
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