I realized that we are by default removing only illumina adapters. Would be good to add a rule that can figure out from the FastQC report whether it is illumina or nextera adapters and if it is nextera then it removes the adapters with:
cutadapt -a CTGTCTCTTATA --minimum-length 30 -o sample.trimmed.fastq.gz sample.merged.fastq.gz -j 10
I realized that we are by default removing only illumina adapters. Would be good to add a rule that can figure out from the FastQC report whether it is illumina or nextera adapters and if it is nextera then it removes the adapters with:
cutadapt -a CTGTCTCTTATA --minimum-length 30 -o sample.trimmed.fastq.gz sample.merged.fastq.gz -j 10