Some fixes on top of feature/support-external-data #12
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KateSakharova
approved these changes
Jul 3, 2024
The assembler and amount of memory can be specified in the samplesheet now. Fixed the bits that were not working with multiples runs per invocation of the pipeline. This needs to be reviews and the results sanity checked.
KateSakharova
requested changes
Jul 4, 2024
| } | ||
| else { | ||
| "single_end": true, | ||
| "assembler": assembler ?: params.assembler, |
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Should we define default assembler to metaspades in nextflow.config? or make assembler required in samplesheet?
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I guess the assembler would still be automatically overridden by the complex rules based on metadata after FASTQC_AFTER?
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the rule still stands:
- the samplesheet assembler will be the first option
- if there is no selected assembler, and it's single end -> megahit
- if there is no selected assembler, and it's paired end -> metaspades
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In samplesheet you can skip assembler and in params you can also skip it because it is optional. So in that code you can end up without any assembler chosen.. That is my point
Ge94
reviewed
Jul 5, 2024
Issue: nf-core/tools#2619 Moved the validation to Groovy.
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