Config¶

The VIP configuration is stored in Nextflow configuration files. An additional configuration file can be supplied on the command-line to overwrite default parameter values, add/update profiles, configure processes and update environment variables.

Parameters¶

key	default	description
GRCh37.reference.fasta	installed	human_g1k_v37
GRCh37.reference.fastaFai	installed
GRCh37.reference.fastaGzi	installed
GRCh38.reference.fasta	installed	GCA_000001405.15_GRCh38_no_alt_analysis_set
GRCh38.reference.fastaFai	installed
GRCh38.reference.fastaGzi	installed

Warning: Please take note of the fact that for a different reference fasta.gz the unzipped referenfasta file is also required. Both the zipped and unzipped fasta should have an index.

FASTQ¶

key	default	description
GRCh37.reference.fastaMmi	installed	for details, see here
GRCh38.reference.fastaMmi	installed	for details, see here

CRAM¶

key	default	description
cram.clair3.illumina.model_name	ilmn	for details, see here
cram.clair3.nanopore.model_name	r941_prom_sup_g5014	for details, see here
cram.clair3.pacbio_hifi.model_name	hifi	for details, see here
cram.sniffles2.GRCh37.tandem_repeat_annotations	installed	for details, see here
cram.sniffles2.GRCh38.tandem_repeat_annotations	installed	for details, see here

VCF¶

key	default	description
vcf.gvcf_merge_preset	gatk_unfiltered	allowed values: [gatk, gatk_unfiltered, deepvariant]
vcf.start		allowed values: [normalize, annotate, classify, filter, inheritance, classify_samples, filter_samples]. for reanalysis this defines from which step to start the workflow
vcf.annotate.annotsv_cache_dir	installed
vcf.annotate.vep_buffer_size	1000	for details, see here
vcf.annotate.vep_cache_dir	installed
vcf.annotate.vep_plugin_dir	installed
vcf.annotate.vep_plugin_hpo	installed
vcf.annotate.vep_plugin_inheritance	installed
vcf.annotate.vep_plugin_vkgl_mode	1	allowed values: [0=full VKGL, 1=public VKGL]. update `vcf.annotate.GRCh38.vep_plugin_vkgl` accordingly
vcf.annotate.GRCh37.capice_model	installed
vcf.annotate.GRCh37.vep_custom_gnomad	installed
vcf.annotate.GRCh37.vep_custom_clinvar	installed
vcf.annotate.GRCh37.vep_custom_phylop	installed
vcf.annotate.GRCh37.vep_plugin_spliceai_indel	installed
vcf.annotate.GRCh37.vep_plugin_spliceai_snv	installed
vcf.annotate.GRCh37.vep_plugin_utrannotator	installed
vcf.annotate.GRCh37.vep_plugin_vkgl	installed
vcf.annotate.GRCh38.capice_model	installed
vcf.annotate.GRCh38.vep_custom_gnomad	installed
vcf.annotate.GRCh38.vep_custom_clinvar	installed
vcf.annotate.GRCh38.vep_custom_phylop	installed
vcf.annotate.GRCh38.vep_plugin_spliceai_indel	installed
vcf.annotate.GRCh38.vep_plugin_spliceai_snv	installed
vcf.annotate.GRCh38.vep_plugin_utrannotator	installed
vcf.annotate.GRCh38.vep_plugin_vkgl	installed	update `vcf.annotate.vep_plugin_vkgl_mode` accordingly
vcf.classify.annotate_labels	0	allowed values: [0=false, 1=true]. annotate variant-consequences with classification tree labels
vcf.classify.annotate_path	1	allowed values: [0=false, 1=true]. annotate variant-consequences with classification tree path
vcf.classify.GRCh37.decision_tree	installed	for details, see here
vcf.classify.GRCh38.decision_tree	installed	for details, see here
vcf.classify_samples.annotate_labels	0	allowed values: [0=false, 1=true]. annotate variant-consequences per sample with classification tree labels
vcf.classify_samples.annotate_path	1	allowed values: [0=false, 1=true]. annotate variant-consequences per sample with classification tree path
vcf.classify_samples.GRCh37.decision_tree	installed	for details, see here
vcf.classify_samples.GRCh38.decision_tree	installed	for details, see here
vcf.filter.classes	VUS,LP,P	for details, see here
vcf.filter.consequences	true	allowed values: [true, false]
vcf.filter_samples.classes	MV,OK	for details, see here
vcf.report.max_records
vcf.report.max_samples
vcf.report.template		for details, see here
vcf.report.GRCh37.genes	installed
vcf.report.GRCh38.genes	installed

Profiles¶

VIP pre-defines two profiles. The default profile is Slurm with fallback to local in case Slurm cannot be discovered.

key	description
local	for details, see here
slurm	for details, see here

Additional profiles (for details, see here) can be added to your configuration file and used on the command-line, for example to run VIP on the Amazon, Azure or Google Cloud.

Process¶

By default, each process gets assigned 4 cpus, 8GB of memory and a max runtime of 4 hours. Depending on your system specifications and your analysis you might need to use updated values. For information on how to update process configuration see the Nextflow documentation. The following sections list all processes and their non-default configuration.

FASTQ¶

process	configuration
concat_fastq	default
concat_fastq_paired_end	default
minimap2_align	cpus=8 memory='16GB' time='23h'
minimap2_align_paired_end	cpus=8 memory='16GB' time='23h'
minimap2_index	cpus=8 memory='16GB' time='23h'

CRAM¶

process	configuration
samtools_addreplacerg	default
clair3_call	cpus=4 memory='8GB' time='5h'
clair3_call_publish	default
manta_call	cpus=4 memory='8GB' time='5h'
manta_call_publish	default
samtools_index	default
sniffles2_call	cpus=4 memory='8GB' time='5h'
sniffles2_combined_call	cpus=4 memory='8GB' time='5h'
sniffles2_call_publish	default

VCF¶

process	configuration
annotate	cpus=4 memory='8GB' time='4h'
annotate_publish	default
classify	memory = '2GB'
classify_publish	default
classify_samples	memory = '2GB'
classify_samples_publish	default
concat	default
convert	default
filter	default
filter_samples	default
index	memory='100MB' time='30m'
inheritance	memory = '2GB'
merge_gvcf	memory='2GB' time='30m'
merge_vcf	default
normalize	default
report	memory = '4GB'
slice	default
split	memory='100MB' time='30m'
stats	default

Environment¶

See https://github.com/molgenis/vip/tree/main/config for an overview of available environment variables. Notably this allows to use different Apptainer containers for the tools that VIP relies on.