preprocess_rnaseq

Basic FASTQ preprocessing for RNA-seq

fastqrnaseqrrnatrimmingsubsamplestrandedness

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/preprocess_rnaseq

Description

Basic FASTQ preprocessing for RNA-seq

Input

name:type

description

pattern

`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

Output

name:type

description

pattern

`reads :file`

Preprocessed fastq reads

*.{fq,fastq}{,.gz}

`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) ]

versions.yml