Add support for "null" params

[paulaidt]

python WfExS-backend.py -L workflow_examples/local_config.yaml config-validate -W ../sarek_nxf_docker_3.5.1.wfex.stage 2025-03-03 12:58:13,721 - [INFO] Setting up docker to /usr/bin/docker (derived from docker) (core: True)
2025-03-03 12:58:13,721 - [INFO] Setting up git to /usr/bin/git (derived from git) (core: False)
2025-03-03 12:58:13,721 - [INFO] Setting up java to /home/paulaiborra/inb_lab/entrust/workflow_testing/WfExS-backend/.pyWEenv/bin/java (derived from java) (core: True)
2025-03-03 12:58:13,721 - [INFO] Setting up singularity to /usr/bin/singularity (derived from singularity) (core: True)
2025-03-03 12:58:13,721 - [INFO] Setting up staticBash to /home/paulaiborra/inb_lab/entrust/workflow_testing/WfExS-backend/.pyWEenv/bin/bash-linux-x86_64 (derived from bash-linux-x86_64) (core: False)
* Command "config-validate".
2025-03-03 12:58:13,984 - [INFO] Validating /home/paulaiborra/inb_lab/entrust/workflow_testing/WfExS-backend/../sarek_nxf_docker_3.5.1.wfex.stage
2025-03-03 12:58:14,079 - [ERROR] ERROR 0 in staging definition block: None is not valid under any of the given schemas

Failed validating 'oneOf' in schema['properties']['params']['patternProperties']['^(?!c-l-a-s-s)[^:;]+$']:
    {'oneOf': [{'type': ['string', 'number', 'boolean']},
               {'type': 'array', 'items': {'type': 'string'}},
               {'type': 'array', 'items': {'type': 'number'}},
               {'type': 'array', 'items': {'type': 'boolean'}},
               {'$ref': '#/definitions/DirFile'},
               {'$ref': '#/definitions/Params'}]}

On instance['params']['snpeff_cache']:
    None
2025-03-03 12:58:14,079 - [ERROR] ERROR 1 in staging definition block: None is not valid under any of the given schemas

Failed validating 'oneOf' in schema['properties']['params']['patternProperties']['^(?!c-l-a-s-s)[^:;]+$']:
    {'oneOf': [{'type': ['string', 'number', 'boolean']},
               {'type': 'array', 'items': {'type': 'string'}},
               {'type': 'array', 'items': {'type': 'number'}},
               {'type': 'array', 'items': {'type': 'boolean'}},
               {'$ref': '#/definitions/DirFile'},
               {'$ref': '#/definitions/Params'}]}

On instance['params']['vep_cache']:
    None

YAML file:

workflow_id: git+https://github.com/nf-core/sarek.git@3.5.1
workflow_config:
  secure: false
  containerType: docker
  nextflow:
    profile:
      - docker
      - test
    maxProcesses: 16
    maxTaskDuration: "24h"
placeholders:
  test_datasets: "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/"
  igenomes_base: "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/"
  genome: "testdata.nf-core.sarek"
# All the inputs must be URLs or CURIEs from identifiers.org
params:
  input:
    c-l-a-s-s: ContentWithURIs
    preferred-name: fastq_single.csv
    url: "https://raw.githubusercontent.com/nf-core/sarek/refs/tags/3.5.1/tests/csv/3.0/fastq_single.csv"
    tabular:
      uri-columns:
        - 5
        - 6
      column-sep: ","
      header-rows: 1
  genome: "{genome}"
  igenomes_base: "{igenomes_base}"
  bcftools_annotations: 
    c-l-a-s-s: File
    url: "{test_datasets}/genomics/sarscov2/illumina/vcf/test2.vcf.gz"
  bcftools_annotations_tbi: 
    c-l-a-s-s: File
    url: "{test_datasets}/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi"
  bcftools_header_lines: 
    c-l-a-s-s: File
    url: "https://raw.githubusercontent.com/nf-core/sarek/refs/tags/3.5.1/tests/config/bcfann_test_header.txt"
  snpeff_cache: null
  vep_cache: null
  sentieon_dnascope_model: 
    c-l-a-s-s: File
    url: "s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model"
  split_fastq: 0         
  tools: "strelka" 

  max_time: "24h"

  genomes:
    testdata.nf-core.sarek:
      dbsnp: 
        c-l-a-s-s: File
        url: "{igenomes_base}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
      dbsnp_tbi: 
        c-l-a-s-s: File
        url: "{igenomes_base}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi"
      dict: 
        c-l-a-s-s: File
        url: "{igenomes_base}/genomics/homo_sapiens/genome/genome.dict"
      fasta: 
        c-l-a-s-s: File
        url: "{igenomes_base}/genomics/homo_sapiens/genome/genome.fasta"
      fasta_fai: 
        c-l-a-s-s: File
        url: "{igenomes_base}/genomics/homo_sapiens/genome/genome.fasta.fai"
      germline_resource: 
        c-l-a-s-s: File
        url: "{igenomes_base}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz"
      germline_resource_tbi: 
        c-l-a-s-s: File
        url: "{igenomes_base}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi"
      intervals: 
        c-l-a-s-s: File
        url: "{igenomes_base}/genomics/homo_sapiens/genome/genome.interval_list"
      known_indels: 
        c-l-a-s-s: File
        url: "{igenomes_base}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz"
      known_indels_tbi: 
        c-l-a-s-s: File
        url: "{igenomes_base}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi"
      ngscheckmate_bed: 
        c-l-a-s-s: File
        url: "{igenomes_base}/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed"
           
  outdir:
    c-l-a-s-s: Directory
    # This hint tells that this parameter is the output directory
    autoFill: true
    autoPrefix: false