pipeline does not generate cnv models

[egenomics]

Description of the bug

The pipeline ends with error with ~120 samples:
A USER ERROR has occurred: Bad input: Filtering removed all intervals. Select less strict filtering criteria.

However it does not generate cnv model or ploidy (a run in cohort mode with the samples provided). Only readcounts are available in folder readcounts (hdf5 format).

Command used and terminal output

nextflow run /playground/nf-core-createpanelrefs_dev/dev \
   -profile singularity \
   --input /playground/dataset_cnvs/samplesheets_sarek/samplesheet_bams_illumina.csv \
   --tools germlinecnvcaller \
   --fasta /corebm/tmp/bams/hg38.fa --dict /corebm/tmp/bams/hg38.dict --fai /corebm/tmp/bams/hg38.fa.fai \
   --outdir /playground/dataset_cnvs/germlinecnvcaller_illumina_reference_nochrM \
   --ploidy_priors /playground/dataset_cnvs/priors.table \
   --padding 250 \
   --bin_length 0 \
   --mappable_regions /playground/dataset_cnvs/Illumina-truseq-rapid-exome_v1.2_hg38_target_orig_nochrM.bed

Relevant files

next.log

System information

nextflow version 23.10.1.5891
Workstation
local executor
singularity
ubuntu 22.04
nf-core/createpanelrefs dev (22/01/2024)

[ramprasadn]

Hi @egenomics Could you run the latest dev and see if it works now?