Skip analysis steps

Skip QC steps

type: boolean

Skip visualisation steps

type: boolean

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.

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

You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.

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})$

Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.

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

type: string

Specifies which analysis type for the pipeline - either build references or analyse data

type: boolean

Path to reference folder

required
type: string

ensembl version

type: integer
default: 105

If set, starfusion references are built from scratch instead of downloaded (default)

type: boolean

Read length

type: integer
default: 100

Build or run all references/analyses

type: boolean

Build or run arriba references/analyses

type: boolean

Path to arriba references

type: string

Path to arriba reference blacklist

type: string

Path to arriba reference protein domain

type: string

Path to arriba output

type: string

Path to ensembl references

type: string

Build or run fusioncatcher references/analyses

type: boolean

Path to fusioncatcher output

type: string

Use limitSjdbInsertNsj with int for fusioncatcher

type: integer

Path to fusioncatcher references

type: string

Feed filtered fusionreport fusions to fusioninspector

type: boolean

Use limitSjdbInsertNsj with int for fusioninspector STAR process

type: integer

Skip fusion-report. --fusioninspector_fusions PATH needed to provide a fusion list as input

type: boolean

Path to a fusion list file built with format GENE1--GENE2

type: string

Build fusionreport references

type: boolean

Path to fusionreport references

type: string

Build or run pizzly references/analyses

type: boolean

Path to pizzly output

type: string

Path to pizzly references

type: string

Build or run squid references/analyses

type: boolean

Path to squid output

type: string

Path to squid references

type: string

Build or run starfusion references/analyses

type: boolean

Path to starfusion output

type: string

Path to starfusion references

type: string

Build or run starindex references/analyses

type: boolean

Path to starindex references

type: string

COSMIC username

type: string

COSMIC password

type: string

Options to adjust read trimming criteria.

Preform trimming of reads, default: false

type: boolean

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

type: string

If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.

See the nf-core website docs for more details.

Path to FASTA genome file.

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

This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.

Path to GTF genome file.

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

Path to GTF genome file.

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

Path to GTF genome file.

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

Path to GTF genome file.

type: string
pattern: ^\S+\.refflat?$

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

If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.

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

Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1

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$

Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'

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*)+$

Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'

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

Display help text.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

The Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.

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})$

An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.

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

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

By default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.

Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.

hidden
type: boolean

Use to pull docker containers to run with singularity

hidden
type: boolean

Sequencing center

hidden
type: string

This will reported in the BAM header as CN

Sequencing platform

hidden
type: string

This will reported in the BAM header as PL.

Whether to ignore the GTF in STAR alignment

hidden
type: boolean

Setting false will use GTF file for STAR alignment