Restart from step variantcalling fails on haplotypecaller

[FriederikeHanssen]

Description of the bug

q

Command used and terminal output

nextflow run nf-core/sarek -r 3.4.2 -latest -profile docker --input data/markduplicates_no_table_local.csv --outdir ./test_single_sample --igenomes_base ../data/references --step variant_calling --tools cnvkit,
 strelka,deepvariant,haplotypecaller -with-tower --save_output_as_bam  --max_memory 4.GB --max_cpus 2 -resume --ngscheckmate_bed false

  ***********************************************************************

  A USER ERROR has occurred: Illegal argument value: Positional arguments were provided ',{chr8_44033745-45877265.bed}' but no positional argument is defined for this tool.

  ***********************************************************************
  Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

Work dir:

### Relevant files

q

### System information

sarek 3.4.2

[maxulysse]

Is this linked to #1550 or not at all?

[FriederikeHanssen]

I am not sure. Need to investigate