seqspec check too strict for corner case

[hitz]

@sidwekhande has an example seqspec: e.g. (https://api.data.igvf.org/configuration-files/IGVFFI0714JZHN/@@download/IGVFFI0714JZHN.yaml.gz but auth required) where the fastq has be demuxed fastqs, our and do not have a truseq_read1 and truseq_read2. However, seqspec starts labeling the fastq sequence starting from the truseq region.

So thesr are submitted truseq regions with the length set to 0, and sequence as null. This triggers:

error 8] None is not of type 'string' in spec['library_spec'][0]['regions'][0]['sequence']
[error 9] None is not of type 'string' in spec['library_spec'][0]['regions'][2]['sequence']

Proposed fix: seqspec check should account for len=0 and ignore this error.

[sbooeshaghi]

Can you post the seqspec file here so that I can test it? I thought I had fixed this previously..

[hitz]

There are other errors as well:
IGVFFI0714JZHN-upgrade3.0.yaml.txt

[sbooeshaghi]

The sequence parameter can be set to '' and the error will go away. This check is already embedded in the spec.schema.json

seqspec/seqspec/schema/seqspec.schema.json

Lines 391 to 411 in 289e7e3

	"if": {
	"properties": {
	"min_len": {
	"const": 0
	}
	}
	},
	"then": {
	"properties": {
	"sequence": {
	"type": "string",
	"pattern": "^[ACGTRYMKSWHBVDNX]*$"
	}
	}
	},
	"else": {
	"properties": {
	"sequence": {
	"type": "string",
	"minLength": 1,
	"pattern": "^[ACGTRYMKSWHBVDNX]+$"