genomic-medicine-sweden/nallo pipeline parameters

Long-read variant calling pipeline

Workflow skip options

Allows skipping certain parts of the pipeline

Parameter	Description	Type	Default
`skip_qc`	Skip QC of reads	`boolean`	False
`skip_snv_calling`	Skip short variant calling	`boolean`	False
`skip_genome_assembly`	Skip genome assembly and assembly variant calling	`boolean`	False
`skip_alignment`	Skip read mapping (alignment)	`boolean`	False
`skip_methylation_pileups`	Skip generation of methylation pileups	`boolean`	False
`skip_repeat_calling`	Skip tandem repeat calling	`boolean`	False
`skip_repeat_annotation`	Skip tandem repeat annotation	`boolean`	False
`skip_phasing`	Skip phasing of variants and haplotagging of reads	`boolean`	False
`skip_snv_annotation`	Skip short variant annotation	`boolean`	False
`skip_sv_annotation`	Skip structural variant annotation	`boolean`	False
`skip_cnv_calling`	Skip CNV calling	`boolean`	False
`skip_call_paralogs`	Skip the calling of specific paralogous genes	`boolean`	False
`skip_rank_variants`	Skip ranking of short variants	`boolean`	False

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 3 columns, and a header row.	`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
`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`
`multiqc_title`	MultiQC report title. Printed as page header, used for filename if not otherwise specified.	`string`
`cadd_prescored_indels`	Path to a directory containing prescored indels for CADD. Help This folder contains the compressed files and indexes that would otherwise be in data/prescored folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation.	`string`
`cadd_resources`	Path to a directory containing CADD annotations. Help This folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation.	`string`
`par_regions`	Provide a bed file of chrX and chrY PAR regions for dipcall and DeepVariant	`string`
`tandem_repeats`	A tandem repeat BED file for sniffles	`string`
`trgt_repeats`	A BED file with repeats to be genotyped with TRGT	`string`
`echtvar_snv_databases`	A csv file with echtvar databases to annotate SNVs with	`string`
`svdb_sv_databases`	Databases used for structural variant annotation in vcf format. Help Path to comma-separated file containing information about the databases used for structural variant annotation.	`string`
`stranger_repeat_catalog`	A variant catalog json-file for stranger	`string`
`variant_consequences_snvs`	File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SNVs. For more information check https://ensembl.org/info/genome/variation/prediction/predicted_data.html	`string`
`variant_consequences_svs`	File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SVs. For more information check https://ensembl.org/info/genome/variation/prediction/predicted_data.html	`string`
`vep_cache`	A path to the VEP cache location	`string`
`target_regions`	A BED file with regions of interest, used to limit variant calling.	`string`
`hificnv_expected_xy_cn`	A BED file containing expected copy number regions for XY samples.	`string`
`hificnv_expected_xx_cn`	A BED file containing expected copy number regions for XX samples.	`string`
`hificnv_excluded_regions`	A BED file specifying regions to exclude with HiFiCNV, such as centromeres.	`string`
`genmod_reduced_penetrance`	A file with gene ids that have reduced penetrance. For use with genmod.	`string`
`genmod_score_config_snvs`	A SNV rank model config file for genmod.	`string`
`genmod_score_config_svs`	A SV rank model config file for genmod.	`string`
`somalier_sites`	A VCF of known polymorphic sites for somalier	`string`
`pipelines_testdata_base_path`	Base URL or local path to location of pipeline test dataset files	`string`	https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/ba720cd29322036d966ab3e4bc4c3d03e1731af5/		True

Reference genome options

Reference genome related files and options required for the workflow.

Parameter	Description	Type	Default	Required	Hidden
`fasta`	Reference genome	`string`

Institutional config options

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

Parameter	Description	Type	Default	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	Hidden
`version`	Display version and exit.	`boolean`		True
`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	True
`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`		True
`multiqc_config`	Custom config file to supply to MultiQC.	`string`		True
`multiqc_logo`	Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file	`string`		True
`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

Workflow options

Workflow options specific to genomic-medicine-sweden/nallo

Parameter	Description	Type	Default	Required	Hidden
`preset`	Enable or disable certain parts of the pipeline by default, depending on data type (`revio`, `pacbio`, `ONT_R10`)	`string`	revio	True
`snv_caller`	Which short variant software to use (`deepvariant`)	`string`	deepvariant
`sv_caller`	Which structural variant caller to use (`severus`, `sniffles`)	`string`	severus
`phaser`	Which phasing software to use (`longphase`, `whatshap`, `hiphase`)	`string`	longphase
`hifiasm_mode`	Run hifiasm in hifi-only or hifi-trio mode (`hifi-only`, `trio-binning`)	`string`	hifi-only
`alignment_processes`	If alignment_processes is bigger than 1, input files will be split and aligned in parallel to reduce processing time.	`integer`	8
`snv_calling_processes`	If snv_calling_processes is bigger than 1, short variant calling will be done in parallel to reduce processing time.	`integer`	13
`vep_cache_version`	VEP cache version	`integer`	110
`vep_plugin_files`	A csv file with vep_files as header, and then paths to vep plugin files. Paths to pLI_values.txt and LoFtool_scores.txt are required.	`string`
`filter_variants_hgnc_ids`	A tsv/csv file with a `hgnc_ids` column header, and then one numerical HGNC ID per row. E.g. `4281` or `HGNC:4281`.	`string`
`filter_snvs_expression`	An expression that is passed to bcftools view to filter SNVs, e.g. --filter_snvs_expression "-e 'INFO/AQ>60'"	`string`
`filter_svs_expression`	An expression that is passed to bcftools view to filter SVs, e.g. --filter_svs_expression "-e 'INFO/AQ>60'"	`string`
`deepvariant_model_type`	Sets the model type used for DeepVariant. This is set automatically using `--preset` by default.	`string`	PACBIO		True
`minimap2_read_mapping_preset`	Sets the minimap2-preset (-x) for read alignment. This is set automatically using the pipeline `--preset` by default.	`string`	map-hifi		True
`extra_modkit_options`	Extra options to modkit, used for test profile.	`string`			True
`extra_vep_options`	Extra options to VEP, used for test profile.	`string`			True
`extra_paraphase_options`	Extra options to Paraphase, used for test profile.	`string`			True
`extra_hifiasm_options`	Extra options to hifiasm, used for test profile.	`string`			True