Introduction Usage Parameters Output Releases

Add ENSEMBL canonical proteomes

Add the reference proteome to the file

type: boolean
default: true

Path to configuration file for ENSEMBL download parameters

type: string

Path to configuration file for parameters in generating protein databases from ENSMEBL sequences

type: string

URL for downloading GENCODE datafiles

type: string
default: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19

Taxonomic term for the species to download from ENSEMBL

type: string
default: homo_sapiens

Non canonical proteins generation parameters

Generate protein database from non-coding RNA

type: boolean

Generate protein database from pseudogenes

type: boolean

Generate alternative ORFs from canonical proteins

type: boolean

Download ENSEMBL variants and generate protein database

type: boolean

Proteins generated using an input VCF

Enable translation of a given VCF file

type: boolean

VCF file path to be translated. Generate variants proteins by modifying sequences of affected transcripts.

type: string

Allele frequency identifier string in VCF Info column, if no AF info is given set it to empty.

type: string

cBioportal variant parameters

Download cBioPortal studies and generate protein database

type: boolean

Specify a tissue type to limit the cBioPortal mutations to a particular caner type

type: string
default: all

Specify a column from the clinical sample file to be used for filtering records

type: string
default: CANCER_TYPE

Download mutations from a specific study in cbiportal default is all which downloads mutations from all studies

type: string

cBioPortal configuration file

type: string

COSMIC variant proteins parameters

Download COSMIC mutation files and generate protein database

type: boolean

Download COSMIC cell line files and generate protein database

type: string

User name (or email) for COSMIC account

type: string

Password for COSMIC account

type: string

Path to configuration file for parameters in generating

type: string

Specify a tissue type to limit the COSMIC mutations to a particular caner type

type: string
default: all

Specify a sample name to limit the COSMIC cell line mutations to a particular cell line

type: string
default: all

Add gNOMAD variants to the database

type: boolean

gNOMAD url

type: string
default: gs://gnomad-public/release/2.1.1/vcf/exomes/gnomad.exomes.r2.1.1.sites.vcf.bgz

Generate decoy proteins and attach them to the final protein database

Append the decoy proteins to the database

type: boolean

String to be used as prefix for the generated decoy sequences

type: string
default: Decoy_

Method used to generate the decoy database

type: string

Enzyme used to generate the decoy

type: string
default: Trypsin

Configuration file to perform the decoy generation

type: string

Clean and process the resulted database

Clean the database for stop codons, short protein sequences

type: boolean

Minimum number of AminoAcids for a protein to be included in the database

type: integer
default: 6

If an stop codons is found, create two proteins from it

type: boolean

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

The output directory where the results will be saved.

type: string
default: ./results

Email address for completion summary.

type: string

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.

Filename for the final protein database

type: string
default: final_proteinDB.fa

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.

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Email address for completion summary, only when pipeline fails.

hidden
type: string

This works exactly as with --email, except emails are only sent if the workflow is not successful.

Send plain-text email instead of HTML.

hidden
type: boolean

Set to receive plain-text e-mails instead of HTML formatted.

File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB

If file generated by pipeline exceeds the threshold, it will not be attached.

Do not use coloured log outputs.

hidden
type: boolean

Set to disable colourful command line output and live life in monochrome.

Directory to keep pipeline Nextflow logs and reports.

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

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.

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

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

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'

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

Git commit id for Institutional configs.

hidden
type: string
default: master

Provide git commit id for custom Institutional configs hosted at nf-core/configs. This was implemented for reproducibility purposes. Default: master.

## Download and use config file with following git commit id  
--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96

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 the custom_config_base option. For example:

## Download and unzip the config files  
cd /path/to/my/configs  
wget https://github.com/nf-core/configs/archive/master.zip  
unzip master.zip  
  
## Run the pipeline  
cd /path/to/my/data  
nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/

Note that the nf-core/tools helper package has a download command to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.

Institutional configs hostname.

hidden
type: string

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
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