DSL1: No fasta indexing when using bowtie2.

[TCLamnidis]

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/eager pipeline documentation
  - 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 or genotyping_ug is submitted.

Expected behaviour

Process for damageprofiler or genotyping_ug is submitted.

Log files

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• The command used to run the pipeline
• The .nextflow.log file
• The exact error:

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Additional context