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When using bowtie2 as the mapper, and not providing a fasta index already, damageprofiler and genotyping is not executed, because the fasta_index is not generated at all.
Check Documentation
I have checked the following places for your error:
- nf-core/eager FAQ/troubleshooting can be found here
Description of the bug
When using bowtie2 as the mapper, and not providing a fasta index already, damageprofiler and genotyping is not executed, because the fasta_index is not generated at all.
Steps to reproduce
Steps to reproduce the behaviour:
nextflow run nf-core/eager -r 2.4.7 -profile test,docker --mapper 'bowtie2' --run_genotyping --genotyping_tool 'ug'
No process for
damageprofiler
orgenotyping_ug
is submitted.Expected behaviour
Process for
damageprofiler
orgenotyping_ug
is submitted.Log files
Have you provided the following extra information/files:
.nextflow.log
fileSystem
Nextflow Installation
Container engine
Additional context
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