fix demultiplex

03_demultiplexing/rules/demultiplexing.smk

@@ -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}
         '''