nf-core/dualrnaseq

Path to comma-separated file containing information about the samples in the experiment.

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

Email address for completion summary.

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

Option to generate mapping statistics, creating plots and summaries

To ignore igenomes reference config

Name of iGenomes reference.

Path to FASTA genome file.

default param???

Change to custom name if desired, ie Human_hela_cells

Change to custom name if desired, ie Salmonella_SL1344

Host genome fasta file

Pathogen genome fasta file

Host GFF file

Pathogen GFF

Host transcriptome file

Pathogen transcriptome file

Define a set of additional fastqc parameters you wish to use, except —quiet —threads —noextract flags which are already specified in the dualrnaseq pipeline

Additional parameters if needed

Options for setting the library type. A = automatic detection

The pipeline uses gene features from the 3rd column of the host annotative file (gff3) to extract the coordinates of transcripts to be quantified. By default, the pipeline useanscriptome_hosts exon from the —gff_host

The pipeline uses gene features from the 3rd column of the pathogen annotative fikle (gff3) to extract the coordinates of transcripts to be quantified. By default, the pipeline uses features as gene, sRNA, tRNA and rRNA from the —gff_pathogen file.

This flag defines the gene attribute from the 9th column of the host annotative (gff3) file, where the transcript names are extracted. By default, the pipeline extracts transcript_id from the —gff_host file

This flag defines the gene attribute from the 9th column of the pathogen annotative (gff3) file, where transcript, genes or CDS regions are extracted. By default, the pipeline extracts locus_tag from the —gff_pathogen file

Still to be described

Still to be described - requires capital P though

Run Salmon selective alignment. Does not need a value, just run —salmon_sa

Set of additional parameters for creating an index with Salmon Selective Alignment. By default, the kmer size is set at 21. Multiple parameters can be passed - for example: —salmon_sa_index_args=“—keepDuplicates -k 21”.

Set of additional parameters for mapping with Salmon Selective Alignment. By default, the pipeline allows soft-clipping of overhanging reads. Multiple parameters can be passed - for example: —salmon_sa_args=“—softclipOverhangs —allowDovetail”

To run Salmon alignment-based mode

STAR parameter - To create a transcriptome Bam (to use with Salmon)

The nf-core/dualrnaseq pipeline runs STAR to generate transcriptomic alignments. By default, it allows for insertions, deletions and soft-clips (Singleend option). To prohibit this behaviour, please specify IndelSoftclipSingleend

Define a set of additional salmon quant parameters you wish to use in salmon alignment-based mode.

To run STAR genome alignment

Quant value in GFF 3rd column

parent attribule in GFF - last column

By default, the pipeline saves unmapped reads within the main BAM file. If you want to switch off this option, set the —outSAMunmapped flag to None

Option to limit RAM when sorting BAM file. If 0, will be set to the genome index size, which can be quite large when running on a desktop or laptop

Additional args to pass to STAR

To run HTSeq count on a aligned genome file

3rd value of GFF to quantify

Gene attributes from the 9th column in GFF to use

Counting mode: Options of ‘union’, ‘intersection-strict’, ‘intersection-nonempty’

For counting non-unique reads. Options of ‘none’, ‘all’, ‘fraction’, ‘random’

Read strand orientation. Options of ‘yes’, ‘no’, ‘reverse’

by default the bam file is sorted by position - Important for PE reads

Features from 3rd column in GFF to use

Gene attributes from the 9th column in GFF to use

Features from 3rd column in GFF to use

Gene attributes from the 9th column in GFF to use

Additional args to pass to HTSeq-count

Custom MultiQC yaml file containing HTML including a methods description.