Error running createpanelrefs

[msierk]

Description of the bug

I'm running createpanelrefs on biowulf and am getting the error below. I can run sarek fine, so it's not a general nextflow issue. log file attached.

Command used and terminal output

run script (have run with and without target bed files, same error occurs):

#! /bin/bash
#SBATCH --job-name=nextflow-main
#SBATCH --cpus-per-task=16
#SBATCH --mem=80gb
#SBATCH --gres=lscratch:200
#SBATCH --time=10-00:00:00

module load nextflow
export NXF_SINGULARITY_CACHEDIR=/data/$USER/singularity;
export SINGULARITY_CACHEDIR=/data/$USER/.singularity;
export TMPDIR=/lscratch/$SLURM_JOB_ID
export NXF_JVM_ARGS="-Xms2g -Xmx4g"

nextflow run nf-core/createpanelrefs -r dev\
	-profile biowulf \
	--input ./PoN_samplesheet.csv \
	--outdir ./PoN \
	--genome GATK.GRCh38 \
	--gcnv_analysis_type wes \
	--tools cnvkit,germlinecnvcaller,mutect2

#--gcnv_target_bed /home/sierkml/nextgen2/runx/nf/data/regions/xgen-exome-hyb-panel-v2-targets-hg38.flank150.bed \
#--mutect2_target_bed /home/sierkml/nextgen2/runx/nf/data/regions/xgen-exome-hyb-panel-v2-targets-hg38.flank150.bed \

Output error:
ERROR ~ Invalid method invocation call with arguments: [[id:null], /fdb/igenomes_nf/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict] (java.util.LinkedList) on _closure6 type

Relevant files

nextflow_11_7_24_log.txt

System information

N E X T F L O W ~ version 24.04.4
HPC (Biowulf)
slurm
Singularity

[msarkis-icr]

Hello,
Is there any update or workaround I can use to run the pipeline.
Please find below the command I'm using:

nextflow run nf-core/createpanelrefs -r dev\
  --input sample_sheet.csv \
  --outdir pon_PRADA \
  --genome GATK.GRCh38 \
  -profile icr_alma \
  --tools mutect2,cnvkit,germlinecnvcaller\

[msarkis-icr]

There is a current pull request #50 that solves this issue (thanks to @maxulysse)
I tested it using some downloaded fasta and dict genome references.

nextflow run maxulysse/nf-core_createpanelrefs -r mutect2_once_more \
  --input sample_sheet.csv \
  --outdir pon_PRADA_mod \
  --fasta /..//Homo_sapiens_assembly38.fasta \
  --dict  /../Homo_sapiens_assembly38.dict \
  --tools mutect2,cnvkit,germlinecnvcaller \
  -c custom.config -resume