When both sentieon_haplotype and haplotypecaller are provided, config scopes are clashing

[FriederikeHanssen]

Description of the bug

#1260 (comment)

Command used and terminal output

No response

Relevant files

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System information

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[asp8200]

It seems like I can reproduce the error with this simple test:

nextflow run main.nf -profile test_cache,software_license,targeted,docker --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper,haplotypecaller --step variant_calling --outdir results

error msg:

The sample-sheet only contains tumor-samples, but the following tools, which were requested by the option "tools", expect at least one normal-sample : haplotypecaller
Process 'CNNSCOREVARIANTS' has been already used -- If you need to reuse the same component, include it with a different name or include it in a different workflow context

 -- Check script './workflows/../subworkflows/local/bam_variant_calling_germline_all/../vcf_variant_filtering_gatk/main.nf' at line: 22 or see '.nextflow.log' file for more details

[asp8200]

The problem seems to go away if I do

include { VCF_VARIANT_FILTERING_GATK                                                   } from '../vcf_variant_filtering_gatk/main'
include { VCF_VARIANT_FILTERING_GATK as SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK } from '../vcf_variant_filtering_gatk/main'

and use SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK for the Sentieon-haplotyper-subworkflow.

Are you okay with that solution? Go ahead an suggest another name than the rather long SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK :-)

[FriederikeHanssen]

yep sounds good, I am god with expressive names. Thanks