subworkflows/preprocess_rnaseq
Basic FASTQ preprocessing for RNA-seq
fastqrnaseqrrnatrimmingsubsamplestrandedness
Input
Name (Type)
Description
Pattern
Channel with input FastQ files of size 1 and 2 for single-end and
paired-end data, respectively.
Channel with text file containing paths to fasta files (one per line)
that will be used to create the database for SortMeRNA
Skip the UMI extraction from the read in case the UMIs have been moved
to the headers in advance of the pipeline run
Specifies the trimming tool to use - available options are ‘trimgalore’
and ‘fastp’
Minimum number of trimmed reads below which samples are removed from
further processing