Basic FASTQ preprocessing for RNA-seq


Name (Type)

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’ ]

ch_reads (file)

Channel with input FastQ files of size 1 and 2 for single-end and
paired-end data, respectively.

ch_fasta (file)

Channel with genome sequence in fasta format

ch_transcript_fasta (file)

Channel with transcriptome sequence in fasta format

ch_gtf (file)

Channel with features in GTF format

ch_salmon_index (file)

Directory containing Salmon index

ch_sortmerna_index (file)

Directory containing sortmerna index

ch_bbsplit_index (file)

Path to directory or tar.gz archive for pre-built BBSplit index

ch_ribo_db (file)

Channel with text file containing paths to fasta files (one per line)
that will be used to create the database for SortMeRNA

skip_bbsplit (boolean)

Whether to skip BBSplit for removal of non-reference genome reads

skip_fastqc (boolean)

Whether to skip FastQC

skip_trimming (boolean)

Whether to skip trimming

skip_umi_extract (boolean)

Skip the UMI extraction from the read in case the UMIs have been moved
to the headers in advance of the pipeline run

make_salmon_index (boolean)

Whether to create salmon index before running salmon quant

make_sortmerna_index (boolean)

Whether to create sortmerna index before running sortmerna

trimmer (string)

Specifies the trimming tool to use - available options are ‘trimgalore’
and ‘fastp’

min_trimmed_reads (integer)

Minimum number of trimmed reads below which samples are removed from
further processing

save_trimmed (boolean)

Save the trimmed FastQ files in the results directory?

remove_ribo_rna (boolean)

Enable the removal of reads derived from ribosomal RNA using SortMeRNA?

with_umi (boolean)

Enable UMI-based read deduplication

umi_discard_read (integer)

After UMI barcode extraction discard either R1 or R2 by setting this
parameter to 1 or 2, respectively


Name (Type)

reads (file)

Preprocessed fastq reads


multiqc_files (file)

MultiQC-compatible output files from tools used in prepreocessing


trim_read_count (integer)

Number of reads remaining after trimming for all input samples

versions (file)

File containing software versions
Structure: [ path(versions.yml) ]