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nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://nf-co.re/sarek
MIT License
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Restart from step variantcalling fails on haplotypecaller #1616

Open FriederikeHanssen opened 2 months ago

FriederikeHanssen commented 2 months ago

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

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### System information

sarek 3.4.2
maxulysse commented 1 month ago

Is this linked to https://github.com/nf-core/sarek/issues/1550 or not at all?

FriederikeHanssen commented 1 month ago

I am not sure. Need to investigate