Introduction Usage Parameters Output Results Releases

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

File containing SRA/ENA/GEO/DDBJ identifiers one per line to download their associated metadata and FastQ files.

type: string
pattern: ^\S+\.(csv|tsv|txt)$

Specifies the type of identifier provided via --input - available options are 'sra' and 'synapse'.

type: string

Comma-separated list of ENA metadata fields to fetch before downloading data.

type: string

The default list of fields used by the pipeline can be found at the top of the bin/sra_ids_to_runinfo.py script within the pipeline repo. This pipeline requires a minimal set of fields to download FastQ files i.e. 'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'. Full list of accepted metadata fields can be obtained from the ENA API.

Comma-separated list of ENA metadata fields used to create a separate 'id_mappings.csv' and 'multiqc_config.yml' with selected fields that can be used to rename samples in general and in MultiQC.

type: string
default: experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description

Name of supported nf-core pipeline e.g. 'rnaseq'. A samplesheet for direct use with the pipeline will be created with the appropriate columns.

type: string

Value for 'strandedness' entry added to samplesheet created when using '--nf_core_pipeline rnaseq'.

type: string
default: auto

The default is 'auto' which can be used with nf-core/rnaseq v3.10 onwards to auto-detect strandedness during the pipeline execution.

Force download FASTQ files via sra-tools instead of via the ENA FTP.

type: boolean

If FTP connections are blocked on your network use this flag to force the pipeline to download data using sra-tools instead of the ENA FTP.

Only download metadata for public data database ids and don't download the FastQ files.

type: boolean
type: string

Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit. Users with granted access to controlled data can download the JWT cart file for the study from the SRA Run Selector upon logging in. The JWT file can only be used on cloud platforms and is valid for 1 hour upon creation.

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})$

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.

Path to Synapse configuration file

hidden
type: string

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

Display version and exit.

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

Do not use coloured log outputs.

hidden
type: boolean

Incoming hook URL for messaging service

hidden
type: string

Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.

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.
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