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Issue with prepare_recalibration and custom genome #267

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maxulysse opened this issue Aug 7, 2020 · 0 comments
Closed

Issue with prepare_recalibration and custom genome #267

maxulysse opened this issue Aug 7, 2020 · 0 comments
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bug Something isn't working
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2.7

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command line:

nextflow run nf-core/sarek -r 2.6.1 --igenomes_ignore --genome custom --input bam.tsv --step prepare_recalibration -profile conda --tools FreeBayes,HaplotypeCaller,mpileup

custom genome:

--fasta genome.fa
--dict genome.dict
--fasta_fai genome.fa.fai
--intervals genome.bed

tsv:

PATIENT  XX  0   SAMPLE /path/to/bam    /path/to/bam.bai
@maxulysse maxulysse self-assigned this Aug 7, 2020
@maxulysse maxulysse added the bug Something isn't working label Aug 7, 2020
@maxulysse maxulysse added this to the 2.6.2 milestone Aug 31, 2020
maxulysse added a commit to maxulysse/nf-core_sarek that referenced this issue Sep 1, 2020
@maxulysse
fix issue with --step prepare_recalibration nf-core#267
8a4e237
maxulysse added a commit to maxulysse/nf-core_sarek that referenced this issue Sep 2, 2020
@maxulysse
fix issue with --prepare_recalibration restart nf-core#267
2f30d73
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