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

Automatic retrieval for restart

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

Specify how many reads each split of a FastQ file contains. Set 0 to turn off splitting at all.

type: integer
default: 50000000

Starting step

type: string

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

required
type: string

Save mapped files.

type: boolean

Save mapped BAMs.

type: boolean

Saves output from Markduplicates & Baserecalibration as BAM file instead of CRAM

type: boolean

True if there are RNA samples to be analysed

type: boolean
default: true

True if there are DNA samples to be analysed

type: boolean
default: true

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

type: string
default: GRCh38

Path to BWA mem indices.

hidden
type: string

Path to bwa-mem2 mem indices.

hidden
type: string

Path to dragmap indices.

hidden
type: string

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

type: string

Splice sites file required for HISAT2.

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 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

Read length

type: number
default: 76

Estimate interval size.

type: number
default: 200000

Path to dbsnp file.

hidden
type: string

Path to dbsnp index.

hidden
type: string

Path to FASTA dictionary file.

hidden
type: string

Path to FASTA genome file.

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

Path to FASTA reference index.

type: string

Path to GATK Mutect2 Germline Resource File.

hidden
type: string

Path to GATK Mutect2 Germline Resource Index.

hidden
type: string

Path to known indels file.

hidden
type: string

Path to known indels file index.

hidden
type: string

If you use AWS iGenomes, this has already been set for you appropriately.

Path to known snps file.

type: string

Path to known snps file snps.

type: string

VEP genome.

hidden
type: string

VEP species.

hidden
type: string

VEP cache version.

hidden
type: number

Save built references.

type: boolean

Only built references.

type: boolean

Download annotation cache.

type: boolean

Directory / URL base for iGenomes references.

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

Do not load the iGenomes reference config.

hidden
type: boolean

Minimum memory required to use splice sites and exons in the HiSAT2 index build process.

type: string
default: 200.GB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

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

Trim fastq file or handle UMIs

Run FastP for read trimming

type: boolean

Remove bp from the 5’ end of read 1

hidden
type: integer

Remove bp from the 5’ end of read 2

hidden
type: integer

Remove bp from the 3’ end of read 1

hidden
type: integer

Remove bp from the 3’ end of read 2

hidden
type: integer

Removing poly-G tails.

hidden
type: integer

Save trimmed FastQ file intermediates.

hidden
type: boolean

If set, publishes split FASTQ files. Intended for testing purposes.

hidden
type: boolean

Define parameters that control the stages in the pipeline

Tools to use for variant calling and/or for annotation.

type: string

Disable specified tools.

type: string

Enable when exome or panel data is provided.

type: boolean

Define parameters related to read alignment

Specify aligner to be used to map reads to reference genome.

type: string

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

Variant callers used to generate calls

type: string
default: sage,strelka,mutect2

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

type: boolean

Disable usage of intervals.

type: boolean

Path to target bed file in case of whole exome or targeted sequencing or intervals file.

type: string

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

type: integer
default: 25

Panel-of-normals VCF (bgzipped) for GATK Mutect2

hidden
type: string

Index of PON panel-of-normals VCF.

hidden
type: string

Runs Mutect2 in joint (multi-sample) mode for better concordance among variant calls of tumor samples from the same patient. Mutect2 outputs will be stored in a subfolder named with patient ID under variant_calling/mutect2/ folder. Only a single normal sample per patient is allowed. Tumor-only mode is also supported.

type: boolean

Bed file with known high confidence used as input in Sage variant caller

hidden
type: string

Bed file with ac actionable list of variants used as input in Sage variant caller

hidden
type: string

Known hotspots used as input in Sage variant caller

hidden
type: string

Directory or tar.gz to ensembl cache for SAGE

hidden
type: string

Directory or tar.gz file to SAGE resources

hidden
type: string

Custom parameters for SAGE

hidden
type: string

Do not analyze soft clipped bases in the reads for GATK Mutect2.

hidden
type: boolean

Allow usage of fasta file for annotation with VEP

hidden
type: boolean

Enable the use of the VEP dbNSFP plugin.

hidden
type: boolean

Path to dbNSFP processed file.

hidden
type: string

Path to dbNSFP tabix indexed file.

hidden
type: string

Consequence to annotate with

hidden
type: string

Fields to annotate with

hidden
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.

hidden
type: boolean

Enable the use of the VEP genesplicer plugin.

type: boolean

Enable the use of the VEP SpliceAI plugin.

hidden
type: boolean

Path to spliceai raw scores snv file.

hidden
type: string

Path to spliceai raw scores snv tabix indexed file.

hidden
type: string

Path to spliceai raw scores indel file.

hidden
type: string

Path to spliceai raw scores indel tabix indexed file.

hidden
type: string

Enable the use of the VEP SpliceRegion plugin.

hidden
type: boolean

Add an extra custom argument to VEP.

hidden
type: string
default: --no_progress --offline --shift_hgvs 1 --check_existing --tsl --domains --total_length --allele_number --no_escape --xref_refseq --failed 1 --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --format vcf --biotype --force_overwrite --sift p --polyphen p --variant_class --regulatory --allele_number --af_gnomad --af_gnomadg --gene_phenotype --hgvs --hgvsg --max_af

Path to VEP cache.

hidden
type: string

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

Path to BED file with variants to whitelist during filtering

type: string

Path to BED file with positions to blacklist during filtering (e.g. regions difficult to map)

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

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

Base path / URL for data used in the test profiles

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

Sequencing center information to be added to read group (CN field).

hidden
type: string

Sequencing platform information to be added to read group (PL field).

hidden
type: string
default: ILLUMINA

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|d|day)\s*)+$

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

Email address for completion summary.

type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

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

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

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

Show all params when using --help

hidden
type: boolean

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

Validation of parameters in lenient more.

hidden
type: boolean

Incoming hook URL for messaging service

hidden
type: string

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

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