Define where the pipeline should find input data and save output data.

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

required
type: string
pattern: ^\S+\.csv$

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

required
type: string

Email address for completion summary.

type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

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

type: string

Reference genome related files and options required for the workflow.

Path to genome FASTA file.

type: string
pattern: ^\S+\.fn?a(sta)?(\.gz|\.zip)?$

Path to transcriptome FASTA file.

type: string
pattern: ^\S+\.fn?a(sta)?(\.gz|\.zip)?$

Path to GTF file.

required
type: string
pattern: ^\S+\.gtf(\.gz|\.zip)?$

Name of iGenomes reference.

type: string

Do not load the iGenomes reference config.

hidden
type: boolean
default: true

The base path to the igenomes reference files

hidden
type: string
default: s3://ngi-igenomes/igenomes/

This is the delimiter the FASTA uses in the sequence identifier to separate the string.

type: string

Options related to processing fastqs

The number of lines to split the FASTQ into.

type: integer

Options to choose trimming criteria and software.

Choose minimum read length.

type: integer
default: 1

Choose minimum average read quality score.

type: integer
default: 10

Skip quality trimming step.

type: boolean

Options related to the barcode and umis.

User-provided file containing a list of cellular barcodes. Using this parameter will override the default whitelists provided by the pipeline and use the user-provided one instead.

type: string

Specify the format for the barcode+umi. This parameter also defines a default barcode whitelist for the pipeline to use for barcode calling, this can be overridden with the ‘whitelist’ parameter.

required
type: string

Specify which tool to be used for deduplication (Options: picard, umitools)

required
type: string

Options related to minimap2.

Library strandness option.

type: string

Minimizer k-mer length.

type: integer
default: 14

Save the secondary alignments when aligning to the genome

type: boolean

Save the secondary alignments when aligning to the transcriptome

type: boolean
default: true

Options related to post-mapping analysis

Indicate whether to include introns in the count matrices

type: boolean
default: true

Provide a comma-delimited options of quantifiers for the pipeline to use. Available tools: isoquant, oarfish

required
type: string

Options to skip various steps within the workflow.

Skip all QC.

type: boolean

Skip FastQC.

type: boolean

Skip Nanoplot.

type: boolean

Skip ToulligQC.

type: boolean

Skip NanoComp from FASTQ file(s).

type: boolean

Skip NanoComp from BAM file(s).

type: boolean

Skip RSeQC.

type: boolean

Skip Seurat QC.

type: boolean

Skip saving minimap2 index.

type: boolean

Skip umi dedup.

type: boolean

Skip MultiQC.

type: boolean

Parameters used to describe centralised config profiles. These should not be edited.

Git commit id for Institutional configs.

hidden
type: string
default: master

Base directory for Institutional configs.

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/configs/master

Institutional config name.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string

Less common options for the pipeline, typically set in a config file.

Display version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

Email address for completion summary, only when pipeline fails.

hidden
type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Send plain-text email instead of HTML.

hidden
type: boolean

File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Do not use coloured log outputs.

hidden
type: boolean

Incoming hook URL for messaging service

hidden
type: string

Custom config file to supply to MultiQC.

hidden
type: string

Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file

hidden
type: string

Custom MultiQC yaml file containing HTML including a methods description.

type: string

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Base URL or local path to location of pipeline test dataset files

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/test-datasets/

Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.

hidden
type: string