params.known_indels curly braces error

[allyssonallan]

Description of the bug

Hey Sarekers,

How are you all? Thanks for your amazing daily support. The validation plugin is blocking the known_indels file and tabix based on the prepare_genome.config specs. The problem I think is based on the curly braces.

https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz

Command used and terminal output

Command:

nextflow run nf-core/sarek -r dev -profile test,singularity -resume -params-file nf-params.json -c nextflow2.config


ERROR ~ Illegal character in path at index 116: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz

 -- Check script '~/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/utils_nfcore_sarek_pipeline/../../nf-core/utils_nfschema_plugin/main.nf' at line: 39 or see '.nextflow.log' file for more details

Relevant files

These are the configs:

known_indels              : [https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz](https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/%7BMills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels%7D.vcf.gz)

  known_indels_tbi          : [https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi](https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/%7BMills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels%7D.vcf.gz.tbi)

This is the prepare_genome.config:

    withName: 'TABIX_KNOWN_INDELS' {
        ext.when         = { !params.known_indels_tbi && params.known_indels && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && (params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') || params.tools.split(',').contains('sentieon_dnascope'))) ) }
        publishDir       = [
            mode: params.publish_dir_mode,
            path: { "${params.outdir}/reference/known_indels" },
            pattern: "*vcf.gz.tbi",
            saveAs: { params.save_reference || params.build_only_index ? it : null }
        ]
    }

    withName: 'TABIX_KNOWN_SNPS' {
        ext.when         = { !params.known_snps_tbi && params.known_snps && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && (params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') )) ) }
        publishDir       = [
            mode: params.publish_dir_mode,
            path: { "${params.outdir}/reference/known_snps" },
            pattern: "*vcf.gz.tbi",
            saveAs: { params.save_reference || params.build_only_index ? it : null }
        ]
    }E

System information

Version: 24.10.4 build 5934
Created: 20-01-2025 16:47 UTC (13:47 BRST)
System: Linux 4.18.0-477.10.1.el8_8.x86_64
Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 17.0.10+7
Encoding: UTF-8 (UTF-8)

HPC
SLURM
Singularity
Sarek 3.5.0

• dev branch

[allyssonallan]

This is the line:

sarek/conf/igenomes.config

Line 64 in ae4dd11

known_indels = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"

[bdvorsky]

I am having exactly the same issue.

[mvsalmon]

I've run into this today as well. Removing the curly braces and setting the filename to
/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz (and the same for the .tbi) seemed to get round the error and start the pipeline. Not sure if it will cause problems later though.