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
default: ./samplesheet.csv
pattern: ^\S+\.csv$

Input sample type. Valid options: ‘DNA’, ‘cDNA’, and ‘directRNA’.

required
type: string

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

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

Options required to basecall and demultiplex samples.

Path to Nanopore run directory files (e.g. ‘fastq_pass/*’) or a basecalled fastq file that requires demultiplexing.

type: string

Barcode kit used to perform the sequencing e.g. ‘SQK-PBK004’.

type: string

Require barcode on both ends for basecaller.

type: boolean

Trim barcodes from the output sequences in the FastQ files from basecaller.

type: boolean

Device specified in GPU mode using ‘—device’.

type: string
default: auto

Cluster options required to use GPU resources (e.g. ‘—part=gpu —gres=gpu:1’).

type: string

Specify the minimum quality score for qcat in the range 0-100.

type: integer
default: 60

Search for adapters in the whole read by applying the ‘—detect-middle’ parameter in qcat.

type: boolean

Skip demultiplexing with qcat.

type: boolean

Filter reads from FastQ files using NanoLyse

type: boolean

Fasta file to be filtered against using NanoLyse

type: string

Options to adjust parameters and filtering criteria for read alignments.

Specifies the aligner to use i.e. ‘minimap2’ or ‘graphmap2’.

type: string
default: minimap2

Specifies if the data is strand-specific. Automatically activated when using ‘—protocol directRNA’.

type: boolean

Save the ‘.sam’ files from the alignment step - not done by default.

type: boolean

Skip alignment and downstream processes.

type: boolean

Options to adjust pameters for DNA varinat calling and structural variant calling.

Specifies if variant calling will executed.

type: boolean

Specifies the variant caller that will used to call small variants (available are: medaka, deepvariant, and pepper_margin_deepvariant). Variant calling is only available if ‘—call_variants’ is set and the protocol is set to DNA. Please note deepvariant and pepper_margin_deepvariant are only avaible if using singularity or docker.

type: string
default: medaka

Specifies the variant caller that will be used to call structural variants (available are: sniffles and cutesv). Structural variant calling is only available if ‘—call_variants’ is set and the protocol is set to DNA.

type: string
default: sniffles

Specifies if MNPs will be split into SNPs when using medaka.

type: boolean

Specifies whether to call variants with pepper_margin_deepvariant in GPU mode.

type: boolean

Specifies if vcf will be phased when using medaka.

type: boolean

Skip variant calling.

type: boolean

Skip structural variant calling.

type: boolean

Options to adjust quantification and differential analysis

Specifies the transcript quantification method to use (available are: bambu or stringtie2). Only available when protocol is cDNA or directRNA.

type: string
default: bambu

Skip transcript quantification and differential analysis.

type: boolean

Skip differential analysis with DESeq2 and DEXSeq.

type: boolean

Options to adjust the RNA fusion analysis

Specifies the reference directory for JAFFAL.

type: string
default: for_jaffal

Skip differential analysis with DESeq2 and DEXSeq.

type: boolean

Options to adjust the RNA modification analysis

Skip RNA modification analysis.

type: boolean

Skip differential modification analysis with xpore.

type: boolean

Skip m6A detection with m6anet.

type: boolean

Options to skip various steps within the workflow.

Skip BigBed file generation.

type: boolean

Skip BigWig file generation.

type: boolean

Skip NanoPlot.

type: boolean

Skip FastQC.

type: boolean

Skip MultiQC.

type: boolean

Skip all QC steps apart from MultiQC.

type: boolean

Reference genome related files and options required for the workflow.

Directory / URL base for iGenomes references.

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

Do not load the iGenomes reference config.

hidden
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

Set the top limit for requested resources for any single job.

Maximum number of CPUs that can be requested for any single job.

hidden
type: integer
default: 16

Maximum amount of memory that can be requested for any single job.

hidden
type: string
default: 128.GB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Maximum amount of time that can be requested for any single job.

hidden
type: string
default: 240.h
pattern: ^(\d+\.?\s*(s|m|h|day)\s*)+$

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

Display help text.

hidden
type: boolean

Display version and exit.

hidden
type: boolean

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

Directory to keep pipeline Nextflow logs and reports.

hidden
type: string
default: ${params.outdir}/pipeline_info

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Show all params when using --help

hidden
type: boolean