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

Save FastQ files after merging re-sequenced libraries in the results directory.

type: boolean

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

type: string

Path to FASTA genome file.

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

Path to FASTA dictionary file.

type: string

Path to FASTA reference index.

type: string

Directory / URL base for iGenomes references.

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

Do not load the iGenomes reference config.

hidden
type: boolean

Path to GTF annotation file.

type: string

Path to GFF3 annotation file.

type: string

Path to BED file containing exon intervals. This will be created from the GTF file if not specified.

type: string

Read length

type: number
default: 151

If generated by the pipeline, save the STAR index in the results directory.

type: boolean

Path to known indels VCF file

type: string

Path to known indels index file

type: string

Path to dbSNP VCF file

type: string

Path to dbSNP VCF index file

type: string

snpEff DB version

type: string

VEP genome

type: string

VEP species

type: string

VEP cache version

type: string

Define parameters related to read alignment

Specifies the alignment algorithm to use. Currently available option is ‘star’

type: string
default: star

Path to STAR index folder or compressed file (tar.gz)

type: string

Enable STAR 2-pass mapping mode.

type: boolean

Do not use GTF file during STAR index buidling step

type: boolean

Option to limit RAM when sorting BAM file. Value to be specified in bytes. If 0, will be set to the genome index size.

type: integer

Specifies the number of genome bins for coordinate-sorting

type: integer
default: 50

Specifies the maximum number of collapsed junctions

type: integer
default: 1000000

Sequencing center information to be added to read group of BAM files.

type: string

Specify the sequencing platform used

type: string
default: illumina

Where possible, save unaligned reads from aligner to the results directory.

type: boolean

Save the intermediate BAM files from the alignment step.

type: boolean

Create a CSI index for BAM files instead of the traditional BAI index. This will be required for genomes with larger chromosome sizes.

type: boolean

Specify whether to remove duplicates from the BAM during Picard MarkDuplicates step.

type: boolean

The minimum phred-scaled confidence threshold at which variants should be called.

type: number
default: 20

Specify which tools RNAvar should use for annotating variants. Values can be ‘snpeff’, ‘vep’ or ‘merge’. If you specify ‘merge’, the pipeline runs both snpeff and VEP annotation.

hidden
type: string

Enable the use of cache for annotation

hidden
type: boolean

Enable CADD cache.

hidden
type: boolean

Path to CADD InDels file.

hidden
type: string

Path to CADD InDels index.

hidden
type: string

Path to CADD SNVs file.

hidden
type: string

Path to CADD SNVs index.

hidden
type: string

Enable the use of the VEP GeneSplicer plugin.

hidden
type: boolean

Path to snpEff cache

hidden
type: string

Path to VEP cache

hidden
type: string

Define parameters that control the stages in the pipeline

Skip the process of base recalibration steps i.e., GATK BaseRecalibrator and GATK ApplyBQSR.

type: boolean

Skip the process of preparing interval lists for the GATK variant calling step

type: boolean

Skip variant filtering of GATK

type: boolean

Skip variant annotation

type: boolean

Skip MultiQC reports

type: boolean

Define parameters of the tools used in the pipeline

Number of times the gene interval list to be split in order to run GATK haplotype caller in parallel

type: integer
default: 25

Do not use gene interval file during variant calling

type: boolean

The window size (in bases) in which to evaluate clustered SNPs.

type: integer
default: 35

The number of SNPs which make up a cluster. Must be at least 2.

type: integer
default: 3

Value to be used for the FisherStrand (FS) filter

type: number
default: 30

Value to be used for the QualByDepth (QD) filter

type: number
default: 2

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

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

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

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

hidden
type: boolean