nf-cmgg/germline pipeline parameters

A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data

Input/output options

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

Parameter	Description	Type	Default	Required	Hidden
input	Path to comma-separated file containing information about the samples in the experiment. Help You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with samples, and a header row. See usage docs.	string		True
outdir	The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.	string		True
watchdir	A folder to watch for the creation of files that start with watch: in the samplesheet.	string
email	Email address for completion summary. Help 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.	string
ped	Path to a pedigree file for all samples in the run. All relational data will be fetched from this file.	string

Reference genome options

Reference genome related files and options required for the workflow.

Parameter	Description	Type	Default	Required	Hidden
genome	Reference genome build. Used to fetch the right reference files. Help Requires a Genome Reference Consortium reference ID (e.g. GRCh38)	string	GRCh38
fasta	Path to FASTA genome file. Help This parameter is mandatory if --genome is not specified. The path to the reference genome fasta.	string		True
fai	Path to FASTA genome index file.	string
dict	Path to the sequence dictionary generated from the FASTA reference. This is only used when haplotypecaller is one of the specified callers.	string
strtablefile	Path to the STR table file generated from the FASTA reference. This is only used when --dragstr has been given.	string
sdf	Path to the SDF folder generated from the reference FASTA file. This is only required when using --validate.	string
elfasta	Path to the ELFASTA genome file. This is used when elprep is part of the callers and will be automatically generated when missing.	string
elsites	Path to the elsites file. This is used when elprep is part of the callers.	string
genomes	Object for genomes	object			True
genomes_base	Directory base for CMGG reference store (used when --genomes_ignore false is specified)	string	/references/
cmgg_config_base	The base directory for the local config files	string	/conf/		True
genomes_ignore	Do not load the local references from the path specified with --genomes_base	boolean			True
igenomes_base	Directory / URL base for iGenomes references.	string			True
igenomes_ignore	Do not load the iGenomes reference config. Help Do not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.	boolean			True

Pipeline specific parameters

Parameters that define how the pipeline works

Parameter	Description	Type	Default	Required	Hidden
scatter_count	The amount of scattering that should happen per sample. Help Increase this number to increase the pipeline run speed, but at the tradeoff of using more IO and disk space. This can differ from the actual scatter count in some cases (especially with smaller files). This has an effect on HaplotypeCaller, GenomicsDBImport and GenotypeGVCFs.	integer	40
merge_distance	The merge distance for family BED files Help Increase this parameter if GenomicsDBImport is running slow. This defines the maximum distance between intervals that should be merged. The less intervals GenomicsDBImport actually gets, the faster it will run.	integer	100000
dragstr	Create DragSTR models to be used with HaplotypeCaller Help This currently is only able to run single-core per sample. Due to this, the process is very slow with only very small improvements to the analysis.	boolean
validate	Validate the found variants	boolean
filter	Filter the found variants.	boolean
annotate	Annotate the found variants using Ensembl VEP.	boolean
add_ped	Add PED INFO header lines to the final VCFs.	boolean
gemini	Create a Gemini databases from the final VCFs.	boolean
mosdepth_slow	Don't run mosdepth in fast-mode Help This is advised if you need exact coverage BED files as output.	boolean
roi	Path to the default ROI (regions of interest) BED file to be used for WES analysis. Help This will be used for all samples that do not have a specific ROI file supplied to them through the samplesheet. Don't supply an ROI file to run the analysis as WGS.	string
dbsnp	Path to the dbSNP VCF file. This will be used to set the variant IDs.	string
dbsnp_tbi	Path to the index of the dbSNP VCF file.	string
somalier_sites	Path to the VCF file with sites for Somalier to use.	string	https://github.com/brentp/somalier/files/3412456/sites.hg38.vcf.gz
only_call	Only call the variants without doing any post-processing.	boolean
only_merge	Only run the pipeline until the creation of the genomicsdbs and output them.	boolean
output_genomicsdb	Output the genomicsDB together with the joint-genotyped VCF.	boolean
callers	A comma delimited string of the available callers. Current options are: haplotypecaller and vardict.	string	haplotypecaller
vardict_min_af	The minimum allele frequency for VarDict when no vardict_min_af is supplied in the samplesheet.	number	0.1
normalize	Normalize the variant in the final VCFs.	boolean
only_pass	Filter out all variants that don't have the PASS filter for vardict. This only works when --filter is also given.	boolean
keep_alt_contigs	Keep all aditional contigs for calling instead of filtering them out before.	boolean
updio	Run UPDio analysis on the final VCFs.	boolean
updio_common_cnvs	A TSV file containing common CNVs to be used by UPDio.	string
automap	Run AutoMap analysis on the final VCFs.	boolean
automap_repeats	BED file with repeat regions in the genome. Help This file will be automatically generated for hg38/GRCh38 and hg19/GRCh37 when this parameter has not been given.	string
automap_panel	TXT file with gene panel regions to be used by AutoMap. Help By default the CMGG gene panel list will be used.	string
automap_panel_name	The panel name of the panel given with --automap_panel.	string	cmgg_bio
hc_phasing	Perform phasing with HaplotypeCaller.	boolean
min_callable_coverage	The lowest callable coverage to determine callable regions.	integer	5
unique_out	Don't change this value	string			True

Institutional config options

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

Parameter	Description	Type	Default	Required	Hidden
custom_config_version	Git commit id for Institutional configs.	string	master		True
custom_config_base	Base directory for Institutional configs. Help 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.	string	https://raw.githubusercontent.com/nf-core/configs/master		True
config_profile_name	Institutional config name.	string			True
config_profile_description	Institutional config description.	string			True
config_profile_contact	Institutional config contact information.	string			True
config_profile_url	Institutional config URL link.	string			True

Generic options

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

Parameter	Description	Type	Default	Required	Hidden
version	Display version and exit.	boolean
publish_dir_mode	Method used to save pipeline results to output directory. Help 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.	string	copy
email_on_fail	Email address for completion summary, only when pipeline fails. Help An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.	string			True
plaintext_email	Send plain-text email instead of HTML.	boolean			True
max_multiqc_email_size	File size limit when attaching MultiQC reports to summary emails.	string	25.MB		True
monochrome_logs	Do not use coloured log outputs.	boolean			True
hook_url	Incoming hook URL for messaging service Help Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.	string
multiqc_title	MultiQC report title. Printed as page header, used for filename if not otherwise specified.	string
multiqc_config	Custom config file to supply to MultiQC.	string
multiqc_logo	Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file	string
multiqc_methods_description	Custom MultiQC yaml file containing HTML including a methods description.	string
validate_params	Boolean whether to validate parameters against the schema at runtime	boolean	True		True
pipelines_testdata_base_path	Base URL or local path to location of pipeline test dataset files	string	https://raw.githubusercontent.com/nf-core/test-datasets/		True

Annotation parameters

Parameters to configure Ensembl VEP and VCFanno

Parameter	Description	Type	Default	Required	Hidden
vep_chunk_size	The amount of sites per split VCF as input to VEP.	integer	50000
species	The species of the samples. Help Must be lower case and have underscores as spaces.	string	homo_sapiens
vep_merged	Specify if the VEP cache is a merged cache.	boolean	True
vep_cache	The path to the VEP cache.	string
vep_dbnsfp	Use the dbNSFP plugin with Ensembl VEP. Help The '--dbnsfp' and '--dbnsfp_tbi' parameters need to be specified when using this parameter.	boolean
vep_spliceai	Use the SpliceAI plugin with Ensembl VEP. Help The '--spliceai_indel', '--spliceai_indel_tbi', '--spliceai_snv' and '--spliceai_snv_tbi' parameters need to be specified when using this parameter.	boolean
vep_spliceregion	Use the SpliceRegion plugin with Ensembl VEP.	boolean
vep_mastermind	Use the Mastermind plugin with Ensembl VEP. Help The '--mastermind' and '--mastermind_tbi' parameters need to be specified when using this parameter.	boolean
vep_maxentscan	Use the MaxEntScan plugin with Ensembl VEP. Help The '--maxentscan' parameter need to be specified when using this parameter.	boolean
vep_eog	Use the custom EOG annotation with Ensembl VEP. Help The '--eog' and '--eog_tbi' parameters need to be specified when using this parameter.	boolean
vep_alphamissense	Use the AlphaMissense plugin with Ensembl VEP. Help The '--alphamissense' and '--alphamissense_tbi' parameters need to be specified when using this parameter.	boolean
vep_version	The version of the VEP tool to be used.	number	105.0
vep_cache_version	The version of the VEP cache to be used.	integer	105
dbnsfp	Path to the dbSNFP file.	string
dbnsfp_tbi	Path to the index of the dbSNFP file.	string
spliceai_indel	Path to the VCF containing indels for spliceAI.	string
spliceai_indel_tbi	Path to the index of the VCF containing indels for spliceAI.	string
spliceai_snv	Path to the VCF containing SNVs for spliceAI.	string
spliceai_snv_tbi	Path to the index of the VCF containing SNVs for spliceAI.	string
mastermind	Path to the VCF for Mastermind.	string
mastermind_tbi	Path to the index of the VCF for Mastermind.	string
alphamissense	Path to the TSV for AlphaMissense.	string
alphamissense_tbi	Path to the index of the TSV for AlphaMissense.	string
eog	Path to the VCF containing EOG annotations.	string
eog_tbi	Path to the index of the VCF containing EOG annotations.	string
vcfanno	Run annotations with vcfanno.	boolean
vcfanno_config	The path to the VCFanno config TOML.	string
vcfanno_lua	The path to a Lua script to be used in VCFanno.	string
vcfanno_resources	A semicolon-seperated list of resource files for VCFanno, please also supply their indices using this parameter.	string