Commit db1cdb50 authored by peguerin's avatar peguerin
Browse files

fix demultiplex

parent 0e77b053
......@@ -20,8 +20,12 @@ rule demultiplexing:
shell:
'''
mkdir -p ../results/03_demultiplexing/01_demultiplexed/{params.dmulti[projet]}/{params.dmulti[marker]}
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]} - 2> {log} > {output}
cat ../results/02_assembly/{params.dmulti[run]}.fastq ../results/02_assembly/{params.dmulti[run]}_rev.fastq 2> {log} | \
cutadapt --discard-untrimmed -m {params.minLen} -g {params.dmulti[barcode5]} -O {params.dmulti[lenBarcode5]} - 2>> {log} | \
cutadapt --discard-untrimmed -m {params.minLen} -g ^{params.dmulti[primer5]} -O {params.dmulti[min_f]} - 2>> {log} | \
cutadapt --discard-untrimmed -m {params.minLen} -a {params.dmulti[barcode3]} -O {params.dmulti[lenBarcode3]} - 2>> {log} | \
cutadapt --discard-untrimmed -m {params.minLen} -a {params.dmulti[primer3]}$ -O {params.dmulti[min_r]} - 2>> {log} | \
cutadapt -M {params.maxLen} - 2>> {log} > {output}
'''
......
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