Commit 0e77b053 authored by peguerin's avatar peguerin
Browse files

fix demultiplex

parent d2f17c80
...@@ -21,11 +21,7 @@ rule demultiplexing: ...@@ -21,11 +21,7 @@ rule demultiplexing:
''' '''
mkdir -p ../results/03_demultiplexing/01_demultiplexed/{params.dmulti[projet]}/{params.dmulti[marker]} 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 | \ 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[barcode5]} -O {params.dmulti[lenBarcode5]} - 2> {log} > {output}
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]} - | \
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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