ERROR - failed to load the meta schema

[AndyBlake]

Description of the bug

All of a sudden sarek stops launching with the error concerning meta schema. Tried updating nextflow, sarek and re pulling sarek to a fresh user

Command used and terminal output

nextflow run nf-core/sarek -r 3.4.0 -profile test

N E X T F L O W  ~  version 23.10.1
Launching `https://github.com/nf-core/sarek` [drunk_jennings] DSL2 - revision: 6aeac929c9 [3.4.0]
Downloading plugin [email protected]
Downloading plugin [email protected]
WARN: The following invalid input values have been detected:

* --input: /home/webadm/.nextflow/assets/nf-core/sarek/tests/csv/3.0/fastq_single.csv
* --step: mapping
* --genome: null
* --igenomes_base: s3://ngi-igenomes/igenomes/
* --snpeff_cache: null
* --vep_cache: null
* --igenomes_ignore: true
* --save_reference: false
* --build_only_index: false
* --download_cache: false
* --no_intervals: false
* --nucleotides_per_second: 200000
* --tools: strelka
* --skip_tools: null
* --split_fastq: 0
* --trim_fastq: false
* --clip_r1: 0
* --clip_r2: 0
* --three_prime_clip_r1: 0
* --three_prime_clip_r2: 0
* --trim_nextseq: 0
* --save_trimmed: false
* --save_split_fastqs: false
* --umi_read_structure: null
* --group_by_umi_strategy: Adjacency
* --aligner: bwa-mem
* --use_gatk_spark: null
* --save_mapped: false
* --save_output_as_bam: false
* --seq_center: null
* --seq_platform: ILLUMINA
* --ascat_ploidy: null
* --ascat_min_base_qual: 20
* --ascat_min_counts: 10
* --ascat_min_map_qual: 35
* --ascat_purity: null
* --cf_ploidy: 2
* --cf_coeff: 0.05
* --cf_contamination: 0
* --cf_contamination_adjustment: false
* --cf_mincov: 0
* --cf_minqual: 0
* --cf_window: null
* --cnvkit_reference: null
* --concatenate_vcfs: false
* --ignore_soft_clipped_bases: false
* --joint_germline: false
* --joint_mutect2: false
* --only_paired_variant_calling: false
* --sentieon_dnascope_emit_mode: variant
* --sentieon_dnascope_pcr_indel_model: CONSERVATIVE
* --sentieon_haplotyper_emit_mode: variant
* --wes: false
* --bcftools_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz
* --bcftools_annotations_index: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi
* --bcftools_header_lines: /home/webadm/.nextflow/assets/nf-core/sarek/tests/config/bcfann_test_header.txt
* --dbnsfp: null
* --dbnsfp_consequence: null
* --dbnsfp_fields: rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF
* --dbnsfp_tbi: null
* --outdir_cache: null
* --spliceai_indel: null
* --spliceai_indel_tbi: null
* --spliceai_snv: null
* --spliceai_snv_tbi: null
* --vep_custom_args: --everything --filter_common --per_gene --total_length --offline --format vcf
* --vep_dbnsfp: null
* --vep_include_fasta: false
* --vep_loftee: null
* --vep_out_format: vcf
* --vep_spliceai: null
* --vep_spliceregion: null
* --vep_version: 110.0-0
* --multiqc_config: null
* --multiqc_title: null
* --multiqc_logo: null
* --max_multiqc_email_size: 25.MB
* --multiqc_methods_description: null
* --outdir: null
* --publish_dir_mode: copy
* --email: null
* --email_on_fail: null
* --plaintext_email: false
* --hook_url: null
* --version: false
* --config_profile_name: Test profile
* --config_profile_description: Minimal test dataset to check pipeline function
* --custom_config_version: master
* --custom_config_base: https://raw.githubusercontent.com/nf-core/configs/master
* --config_profile_contact: null
* --config_profile_url: null
* --test_data_base: https://raw.githubusercontent.com/nf-core/test-datasets/sarek3
* --max_memory: 6.5GB
* --max_cpus: 2
* --max_time: 8.h
* --validate_params: true
* --dbsnp: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz
* --fasta: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta
* --germline_resource: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz
* --intervals: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.interval_list
* --known_indels: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz
* --ngscheckmate_bed: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed
* --snpeff_db: 105
* --snpeff_genome: WBcel235
* --vep_cache_version: 110
* --vep_genome: WBcel235
* --vep_species: caenorhabditis_elegans
* --sentieon_dnascope_model: s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model
* --ascat_alleles: null
* --ascat_genome: null
* --ascat_loci: null
* --ascat_loci_gc: null
* --ascat_loci_rt: null
* --bwa: null
* --bwamem2: null
* --cf_chrom_len: null
* --chr_dir: null
* --dbsnp_tbi: null
* --dbsnp_vqsr: null
* --dict: null
* --dragmap: null
* --fasta_fai: null
* --germline_resource_tbi: null
* --known_indels_tbi: null
* --known_indels_vqsr: null
* --known_snps: null
* --known_snps_tbi: null
* --known_snps_vqsr: null
* --mappability: null
* --pon: null
* --pon_tbi: null
* --input_restart: null


ERROR ~ Failed to load the meta schema:
The used schema draft (http://json-schema.org/draft-07/schema) is not correct, please use "https://json-schema.org/draft/2020-12/schema" instead.
See here for more information: https://json-schema.org/specification#migrating-from-older-drafts


 -- Check '.nextflow.log' file for details

Relevant files

Feb-20 16:04:04.226 [main] ERROR n.validation.JsonSchemaValidator - Failed to load the meta schema:
The used schema draft (http://json-schema.org/draft-07/schema) is not correct, please use "https://json-schema.org/draft/2020-12/schema" instead.
See here for more information: https://json-schema.org/specification#migrating-from-older-drafts

Feb-20 16:04:04.229 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_3b23d717def1bedf: /home/webadm/.nextflow/assets/nf-core/sarek/main.nf
Feb-20 16:04:04.229 [main] DEBUG nextflow.Session - Session aborted -- Cause: nextflow.validation.SchemaValidationException:
Feb-20 16:04:04.241 [main] DEBUG nextflow.cli.Launcher - Operation aborted
nextflow.validation.SchemaValidationException:
at nextflow.validation.JsonSchemaValidator.validateObject(JsonSchemaValidator.groovy:43)
at nextflow.validation.JsonSchemaValidator.validate(JsonSchemaValidator.groovy:109)
at nextflow.validation.SchemaValidator.validateParameters(SchemaValidator.groovy:344)
at nextflow.validation.SchemaValidator.validateParameters(SchemaValidator.groovy)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at nextflow.script.FunctionDef.invoke_a(FunctionDef.groovy:64)
at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:40)
at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:102)
at groovy.lang.GroovyObject$invokeMethod.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:148)
at nextflow.script.BaseScript.invokeMethod(BaseScript.groovy:140)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:68)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:176)
at Script_3b23d717def1bedf.runScript(Script_3b23d717def1bedf:92)
at nextflow.script.BaseScript.run0(BaseScript.groovy:144)
at nextflow.script.BaseScript.run(BaseScript.groovy:192)
at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:236)
at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:242)
at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:137)
at nextflow.cli.CmdRun.run(CmdRun.groovy:372)
at nextflow.cli.Launcher.run(Launcher.groovy:500)
at nextflow.cli.Launcher.main(Launcher.groovy:672)

System information

latest, ubuntu 22, local

[FriederikeHanssen]

Hey! Can you try pinning the nf-validation version with adding this to a config and then add the file with -c to your command:

plugins {
    id '[email protected]'
}

[ewels]

We just reverted the plugin release, this problem should now resolve itself.

We will release another day, but try to ensure that all pipelines are properly prepared before doing so.

Shout if anyone is still hitting this after I post this message.

[ewels]

x-ref: nextflow-io/plugins#66