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|tsv|yaml|yml|json)$

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

required
type: string

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

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.

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

Path to FASTA dictionary file.

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

Path to FASTA reference index.

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

Path to GTF annotation file.

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

Path to GFF3 annotation file.

type: string
pattern: ^\S+\.gff\d?$

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

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

Read length

type: number
default: 150

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

type: boolean

Path to known indels VCF file(s)

type: string

Path to known indels index file(s)

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: integer,string

Type of feature to parse from annotation file

type: string

Download annotation cache.

type: boolean

Do not load the iGenomes reference config.

hidden
type: boolean

The base path to the igenomes reference files

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

Parameters for postprocessing of alignment files.

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

type: boolean

Define parameters related to read alignment

Specifies the alignment algorithm to use.

type: string

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 building 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

Specifies the maximum intron size

type: integer

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

Parameters for preprocessing FASTQ files before alignment.

Specify whether to remove UMIs from the reads with UMI-tools extract.

type: boolean

UMI pattern to use. Can be either ‘string’ (default) or ‘regex’.

type: string

The UMI barcode pattern to use e.g. ‘NNNNNN’ indicates that the first 6 nucleotides of the read are from the UMI.

type: string
pattern: ^[NXC]*$

The UMI barcode pattern to use if the UMI is located in read 2.

type: string
pattern: ^[NXC]*$

The character that separates the UMI in the read name. Most likely a colon if you skipped the extraction with UMI-tools and used other software.

type: string

Parameters for variant calling tools.

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

type: integer
default: 20

Enable generation of GVCFs by sample additionnaly to the VCFs.

type: boolean

Parameters for variant annotation tools.

Path to VEP cache.

type: string
default: s3://annotation-cache/vep_cache/

Path to snpEff cache.

type: string
default: s3://annotation-cache/snpeff_cache/

Allow usage of fasta file for annotation with VEP

hidden
type: boolean

Enable the use of the VEP dbNSFP plugin.

type: boolean

Path to dbNSFP processed file.

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

Path to dbNSFP tabix indexed file.

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

Consequence to annotate with

type: string

Fields to annotate with

type: string
default: rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF

Enable the use of the VEP LOFTEE plugin.

type: boolean

Enable the use of the VEP SpliceAI plugin.

type: boolean

Path to spliceai raw scores snv file.

type: string
pattern: ^\S+\.vcf\.gz$

Path to spliceai raw scores snv tabix indexed file.

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

Path to spliceai raw scores indel file.

type: string
pattern: ^\S+\.vcf\.gz$

Path to spliceai raw scores indel tabix indexed file.

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

Enable the use of the VEP SpliceRegion plugin.

type: boolean

Add an extra custom argument to VEP.

type: string
default: --everything --filter_common --per_gene --total_length --offline --format vcf

Use annotation cache keys for snpeff_cache and vep_cache. Only when using annotation-cache or a similar structure. See here for more information.

hidden
type: boolean

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

hidden
type: string

VEP output-file format.

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

Skip the check of the exon bed

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

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

Display version and exit.

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

Incoming hook URL for messaging service

hidden
type: string

Custom config file to supply to MultiQC.

hidden
type: string

Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file

hidden
type: string

Custom MultiQC yaml file containing HTML including a methods description.

type: string

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Base URL or local path to location of pipeline test dataset files

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/

Base URL or local path to location of pipeline test dataset files

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/test-datasets/rnavar/data/

Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.

hidden
type: string