Input¶

The --input value is a tab-separated file (sample-sheet) with each row describing the data and metadata of a sample.

A minimal sample-sheet for the vcf workflow could look like this:

individual_id	vcf
sample0	sample0.vcf.gz
sample1	sample1.vcf.gz
sample2	sample2.vcf.gz

Sample-sheet values are case sensitive. Columns can contain values of different types:

type	description
boolean	allowed values: [true, false]
enum	categorical value
file	absolute file path or file path relative to the sample sheet
file list	comma-separated list of file paths
string	text
string list	comma-separated list of strings

The following sections describe the columns that can be used in every sample-sheet followed by workflow specific columns.

Columns¶

column	type	scope	required	default	description
project_id	string	project		vip	project identifier
family_id	string	family		fam<index>	family identifier
individual_id	string	sample	yes		sample identifier of the individual
paternal_id	string	family			sample identifier of the father
maternal_id	string	family			sample identifier of the mother
sex	enum	sample		unknown sex	values: [male,female] Please note that an unknown sex leads to a Spectre CNV analysis that assumes female for the ploidy determination of chromosome X.
affected	boolean	sample		unknown affected status	whether the individual is affected
proband	boolean	sample		depends1	individual being reported on
hpo_ids	string list	sample			regex: /HP:\d{7}/ from HPO v2024-08-13. term must be a child of 'Phenotypic abnormality' (HP:0000118)
sequencing_method	enum	project		WGS	allowed values: [WES,WGS]
regions	file	project			allowed file extensions: [bed]. filter variants overlapping with regions in bed file
pcr_performed	boolean	project	false	false	Indication if PCR was performed to get the data, if so certain tools will be disabled due to not being compatible with this data.

¹ Exception: if no probands are defined in the sample-sheet then all samples are considered to be probands.

Columns: FASTQ¶

column	type	scope	required	default	description
adaptive_sampling	file	sample			allowed file extensions: [csv]. for nanopore adaptive sampling experiments, used to filter stop_receiving3 or sequence3 reads
fastq	file list	sample	yes2		allowed file extensions: [fastq, fastq.gz, fq, fq.gz]. single-reads file(s)
fastq_r1	file list	sample	yes2		allowed file extensions: [fastq, fastq.gz, fq, fq.gz]. paired-end reads file(s) #1
fastq_r2	file list	sample	yes2		allowed file extensions: [fastq, fastq.gz, fq, fq.gz]. paired-end reads file(s) #2
sequencing_platform	enum	project		nanopore	allowed values: [illumina,nanopore,pacbio_hifi]

² Either the fastq or the fastq_r1 and fastq_r2 are required. ³ stop_receiving when Nanopore output adaptive sampling file specification < 0.1 was used, sequence for version 0.1 and above.

Columns: CRAM¶

column	type	scope	required	default	description
cram	file	sample	yes		allowed file extensions: [bam, cram, sam]
sequencing_platform	enum	project		nanopore	allowed values: [illumina,nanopore,pacbio_hifi]

Columns: gVCF¶

column	type	scope	required	default	description
assembly	enum	project		GRCh38	allowed values: [GRCh37, GRCh38, T2T]
gvcf	file	sample	yes		allowed file extensions: [gvcf, gvcf.gz, gvcf.bgz, vcf, vcf.gz, vcf.bgz, bcf, bcf.gz, bcf.bgz]
cram	file	sample			allowed file extensions: [bam, cram, sam]

Columns: VCF¶

column	type	scope	required	default	description
assembly	enum	project		GRCh38	allowed values: [GRCh37, GRCh38, T2T]
vcf	file	project	yes		allowed file extensions: [vcf, vcf.gz, vcf.bgz, bcf, bcf.gz, bcf.bgz]
cram	file	sample			allowed file extensions: [bam, cram, sam]