The FASTQ read identifiers supplied by the SRA look like @SRR#######.#, but the default readNamePattern used in the demulti and filt rules just takes the portion before the period which leads to errors due to non-unique read IDs. Since the R scripts allow custom patterns it looks like exposing the pattern argument to the rules would allow this to work.
The FASTQ read identifiers supplied by the SRA look like
@SRR#######.#
, but the default readNamePattern used in the demulti and filt rules just takes the portion before the period which leads to errors due to non-unique read IDs. Since the R scripts allow custom patterns it looks like exposing the pattern argument to the rules would allow this to work.