$ mkdir test_verifybamid
$ cd test_verifybamid
$ conda create -y -c bioconda verifybamid2 -p ./conda  # for verifybamid resources
$ nf-core create  # example empty pipeline with verifybamid2
$ cd test-pipeline
$ nf-core modules install verifybamid/verifybamid2
$ rm workflows/pipeline.nf  # simplify down to a single workflow script that calls the module
$ vi main.nf
$ cat main.nf
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { VERIFYBAMID_VERIFYBAMID2 } from './modules/nf-core/verifybamid/verifybamid2/main'                                          

workflow {
  ch_bam = Channel.fromPath(params.bam, checkIfExists: true)
  ch_bai = Channel.fromPath(params.bai, checkIfExists: true)
  VERIFYBAMID_VERIFYBAMID2(
    ch_bam.combine(ch_bai).map({bam, bai -> [[id: bam.name], bam, bai]}),                                                        
    Channel.value(
      [
        file(params.svd_ud, checkIfExists: true),
        file(params.svd_mu, checkIfExists: true),
        file(params.svd_bed, checkIfExists: true)
      ]
    ),
    Channel.fromPath(params.ref_vcf, checkIfExists: true),
    Channel.fromPath(params.ref_fasta, checkIfExists: true)
  )
}
$ nextflow run main.nf -profile singularity \
  --ref_vcf path/to/ref.vcf.gz \
  --ref_fasta path/to/hg38.fa \
  --svd_ud path/to/conda/share/verifybamid2-2.0.1-10/resource/1000g.phase3.10k.b38.vcf.gz.dat.UD \
  --svd_mu path/to/conda/share/verifybamid2-2.0.1-10/resource/1000g.phase3.10k.b38.vcf.gz.dat.mu \
  --svd_bed path/to/conda/share/verifybamid2-2.0.1-10/resource/1000g.phase3.10k.b38.vcf.gz.dat.bed \
  --bam path/to/test.bam \
  --bai path/to/test.bam.bai

N E X T F L O W  ~  version 23.04.1
Launching `main.nf` [shrivelled_gauss] DSL2 - revision: 6f25f6a1e6
executor >  slurm (1)
...
ERROR ~ Error executing process > 'VERIFYBAMID_VERIFYBAMID2 (${meta.id})'

Caused by:
  Process `VERIFYBAMID_VERIFYBAMID2 (${meta.id})` terminated with an error exit status (255)

Command executed:

  verifybamid2 \
      --NumThread 2 \
      --SVDPrefix 1000g.phase3.10k.b38.vcf.gz.dat \
      --BamFile test.bam \
       \
        \
       \
      > test.bam.log

  cat <<-END_VERSIONS > versions.yml
  "VERIFYBAMID_VERIFYBAMID2":
      verifybamid: $(echo $(verifybamid2 --help 2>&1 | sed -e '3p;d' | sed -e 's/ Version://'))
  END_VERSIONS

Command exit status:
  255

Command output:
  (empty)

Command error:
  VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

   Version:2.0.1
   Copyright (c) 2009-2020 by Hyun Min Kang and Fan Zhang
   This project is licensed under the terms of the MIT license.

  The following parameters are available.  Ones with "[]" are in effect:

  Available Options
                      Input/Output Files : --BamFile [test.bam],
                                           --PileupFile [Empty],
                                           --Reference [Empty],
                                           --SVDPrefix [1000g.phase3.10k.b38.vcf.gz.dat],
                                           --Output [result]
                 Model Selection Options : --WithinAncestry,
                                           --DisableSanityCheck, --NumPC [2],
                                           --FixPC [Empty],
                                           --FixAlpha [-1.0e+00],
                                           --KnownAF [Empty], --NumThread [2],
                                           --Seed [12345], --Epsilon [1.0e-08],
                                           --OutputPileup, --Verbose
     Construction of SVD Auxiliary Files : --RefVCF [Empty]
                          Pileup Options : --min-BQ [13], --min-MQ [2],
                                           --adjust-MQ [40], --max-depth [8000],
                                           --no-orphans, --incl-flags [1040],
                                           --excl-flags [1796]
                      Deprecated Options : --UDPath [Empty], --MeanPath [Empty],
                                           --BedPath [Empty]

  FATAL ERROR -
  --Reference is required

    Exiting due to ERROR:
        Exception was thrown

Work dir:
  /mnt/e1000/home/u035/u035/mwham2/test-verifybamid/nf-core/test-testpipeline/work/60/9a4a0eb1a469967e6aa5fc8e3b7ab0

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

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