Previously, when run with $n$ samples and $m$ primers, this workflow ran $n*m$ Cutadapt processes for every possible sample-primer pair. Now, the workflow takes all primers as a single, space-delimited input into a single Cutadapt process depending on how many artifacts the samples are split into. As it turns out, native Cutadapt allows for this and selects the best trimmed output; this is unclear in the q2-cutadapt docs.
SPLIT_FASTQ_MANIFEST is brought back to offer users the option to run sample sets as a single FASTQ artifact or multiple to optimize processing speed.
Closes #83.
Previously, when run with $n$ samples and $m$ primers, this workflow ran $n*m$ Cutadapt processes for every possible sample-primer pair. Now, the workflow takes all primers as a single, space-delimited input into a single Cutadapt process depending on how many artifacts the samples are split into. As it turns out, native Cutadapt allows for this and selects the best trimmed output; this is unclear in the q2-cutadapt docs.
SPLIT_FASTQ_MANIFESTis brought back to offer users the option to run sample sets as a single FASTQ artifact or multiple to optimize processing speed.