The pipeline ran successfully with the GATK.GRCh38 reference. Now I need a run with GATK.GRCh37 for comparison. However, running it with GATK.GRCh37 results in the following error:
Downloading plugin nf-amazon@3.4.4
ERROR ~ Validation of pipeline parameters failed!
-- Check 'nextflow.log' file for details
The following invalid input values have been detected:
* --intervals (s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Annotation/intervals/wgs_calling_regions_Sarek.list): "s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Annotation/intervals/wgs_calling_regions_Sarek.list" does not match regular expression [\S+\.(bed|interval_list)$]
Command:
nextflow -c nextflow_sarek.config -log nextflow.log \
run nf-core/sarek -profile singularity \
-work-dir work -resume \
--input sample_sheet.csv \
--genome GATK.GRCh37 \
--trim-fastq --detect_adapter_for_pe \
--tools haplotypecaller\
--joint_germline \
--filter_vcfs \
--outdir run2
Terminal Output:
Downloading nextflow dependencies. It may require a few seconds, please wait ..
�[K�[33mNextflow 26.04.2 is available - Please consider updating your version to it�(B�[m
N E X T F L O W ~ version 25.10.4
WARN: It appears you have never run this project before -- Option `-resume` is ignored
Downloading plugin nf-core-utils@0.4.0
Downloading plugin nf-fgbio@1.0.0
Downloading plugin nf-prov@1.2.2
Downloading plugin nf-schema@2.6.1
Launching `https://github.com/nf-core/sarek` [intergalactic_morse] DSL2 - revision: 4bd2948f98 [master]
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nf-core/sarek 3.8.1
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Input/output options
input : sample_sheet_v2.csv
outdir : run2/
Main options
intervals : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Annotation/intervals/wgs_calling_regions_Sarek.list
tools : haplotypecaller
Variant Calling
joint_germline : true
Post variant calling
filter_vcfs : true
Reference genome options
genome : GATK.GRCh37
ascat_genome : hg19
ascat_alleles : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/G1000_alleles_hg19.zip
ascat_loci : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/G1000_loci_hg19.zip
ascat_loci_gc : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/GC_G1000_hg19.zip
ascat_loci_rt : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/RT_G1000_hg19.zip
bwa : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/
chr_dir : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Sequence/Chromosomes
dbsnp : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf.gz
dbsnp_tbi : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf.gz.tbi
dbsnp_vqsr : --resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_138.b37.vcf.gz
dict : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.dict
fasta : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta
fasta_fai : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta.fai
germline_resource : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/af-only-gnomad.raw.sites.vcf.gz
germline_resource_tbi: s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/af-only-gnomad.raw.sites.vcf.gz.tbi
known_indels : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.gz
known_indels_tbi : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.gz.tbi
known_indels_vqsr : --resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_phase1.indels.b37.vcf.gz --resource:mills,known=false,training=true,truth=true,prior=10.0 Mills_and_1000G_gold_standard.indels.b37.vcf.gz
known_snps : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/1000G_phase1.snps.high_confidence.b37.vcf.gz
known_snps_tbi : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/1000G_phase1.snps.high_confidence.b37.vcf.gz.tbi
known_snps_vqsr : --resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_phase1.snps.high_confidence.b37.vcf.gz
mappability : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Annotation/Control-FREEC/out100m2_hg19.gem
msisensor2_models : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Annotation/MSIsensor2/models_hg19_GRCh37/
msisensorpro_scan : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Annotation/MSIsensorPro/human_g1k_v37_decoy.msisensor_scan.list
ngscheckmate_bed : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Annotation/NGSCheckMate/SNP_GRCh37_hg19_woChr.bed
snpeff_db : GRCh37.87
vep_cache_version : 115
vep_genome : GRCh37
vep_species : homo_sapiens
Generic options
trace_report_suffix : 2026-05-27_11-56-41
Core Nextflow options
revision : master
runName : intergalactic_morse
containerEngine : singularity
launchDir : run
workDir : run2/work
projectDir : sarek
profile : singularity
configFiles : nextflow.config, nextflow_sarek.config
!! Only displaying parameters that differ from the pipeline defaults !!
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* The pipeline
https://doi.org/10.12688/f1000research.16665.2
https://doi.org/10.1093/nargab/lqae031
https://doi.org/10.5281/zenodo.3476425
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/sarek/blob/master/CITATIONS.md
Downloading plugin nf-amazon@3.4.4
ERROR ~ Validation of pipeline parameters failed!
-- Check 'run2/nextflow.log' file for details
The following invalid input values have been detected:
* --intervals (s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Annotation/intervals/wgs_calling_regions_Sarek.list): "s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Annotation/intervals/wgs_calling_regions_Sarek.list" does not match regular expression [\S+\.(bed|interval_list)$]
-- Check script '/prj/cfngs-sw/nextflow_wfs/nf-core/sarek/subworkflows/nf-core/utils_nfschema_plugin/main.nf' at line: 68 or see 'run2/nextflow.log' file for more details
Description of the bug
The pipeline ran successfully with the GATK.GRCh38 reference. Now I need a run with GATK.GRCh37 for comparison. However, running it with GATK.GRCh37 results in the following error:
Command used and terminal output
Relevant files
No response
System information
Nextflow 25.10.4
Hardware: HPC
Executor: slurm
Container engine: Singularity
OS: Ubuntu 24.04.4 LTS
Version of nf-core/sarek: 3.8.1