DSL2: Ensure modules config consistency: all modules have an `ext.prefix` and `publishDir` attribute, and follow conventions.
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Description
Best for publishDir to be explicitly on/off, and all modules (even when not publishing) need an ext.prefix, now that we don't have meta.id anymore.
Also ensure that all module configurations follow the code conventions (attribute order etc)
Results from quick check on 26/04/2024:
HOST_REMOVAL: has no ext.prefixSAMTOOLS_INDEX_BAM_INPUT: has neitherSAMTOOLS_VIEW_GENOME: no ext.prefixSAMTOOLS_INDEX_DAMAGE_RESCALED: no ext.prefixSAMTOOLS_INDEX_DAMAGE_FILTERED: no ext.prefixSAMTOOLS_INDEX_DAMAGE_TRIMMED: no ext.prefixANGSD_DOCOUNTS: wrong attribute orderMTNUCRATIO: no ext.prefixQUALIMAP_BAMQC_WITHBED|QUALIMAP_BAMQC_NOBED: no ext.prefixSAMTOOLS_DEPTH_SEXDETERRMINE: wrong attribute order
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First steps
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Research direction
Search the DSL2 module configurations for HOST_REMOVAL, SAMTOOLS_INDEX_BAM_INPUT, SAMTOOLS_VIEW_GENOME, SAMTOOLS_INDEX_DAMAGE_RESCALED, SAMTOOLS_INDEX_DAMAGE_FILTERED, SAMTOOLS_INDEX_DAMAGE_TRIMMED, ANGSD_DOCOUNTS, MTNUCRATIO, QUALIMAP_BAMQC_WITHBED, QUALIMAP_BAMQC_NOBED, and SAMTOOLS_DEPTH_SEXDETERRMINE. Compare them with neighboring module configurations and finish when every module has ext.prefix and an explicit publishDir setting, with attributes in the established order.
Written by the indexing model from the issue text.
Assessment
- Domain
- tooling
- Issue type
- Refactor
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100