Using this script with the latest version of the schema in nf-core/sarek creates requirements that currently prevent registration with AWS HealthOmics.
The following specifications are currently not allowed in AWS HealthOmics. So it seems like we need something to either check this as an error or guide us to fix it.
An error occurred (ValidationException) when calling the CreateWorkflow operation: 4 validation errors detected: Value 'Runs Mutect2 in joint (multi-sample) mode for better concordance among variant calls of tumor samples from the same patient. Mutect2 outputs will be stored in a subfolder named with patient ID under variant_calling/mutect2/ folder. Only a single normal sample per patient is allowed. Tumor-only mode is also supported.' at 'parameterTemplate.joint_mutect2.member.description' failed to satisfy constraint: Member must have length less than or equal to 256; Value 'If you use AWS iGenomes, this has already been set for you appropriately.
1st label string for VariantRecalibration (haplotypecaller joint variant calling)' at 'parameterTemplate.known_indels_vqsr.member.description' failed to satisfy constraint: Member must satisfy regular expression pattern: [\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+; Value 'If you use AWS iGenomes, this has already been set for you appropriately.
label string for VariantRecalibration (haplotypecaller joint variant calling)' at 'parameterTemplate.known_snps_vqsr.member.description' failed to satisfy constraint: Member must satisfy regular expression pattern: [\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+; Value 'If you use AWS iGenomes, this has already been set for you appropriately.
Path to known snps file.' at 'parameterTemplate.known_snps.member.description' failed to satisfy constraint: Member must satisfy regular expression pattern: [\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+
Firstly, thank you for the useful script.
create_parameter_json_from_nfcore_schema.py
Using this script with the latest version of the schema in nf-core/sarek creates requirements that currently prevent registration with AWS HealthOmics.
https://github.com/nf-core/sarek/blob/3.4.2/nextflow_schema.json
The following specifications are currently not allowed in AWS HealthOmics. So it seems like we need something to either check this as an error or guide us to fix it.