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Replaces dnaSeqExperimentFromAccession and dnaSeqExperimentFromLocal with a single dnaseqExperiment datasetTemplate modeled after longReadRnaSeqExperiment. Adds snpAndCnvDNASeq.xml workflow (processSingleExperiment + loadSingleExperiment via dnaseq-nextflow), MakeDnaSeqNextflowConfig.pm, and MakeDnaSeqLoadNextflowConfig.pm. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…o organism level - Remove trimmomaticAdaptorsFile, freebayesMinAltFraction, maxNumberOfReads from MakeDnaSeqNextflowConfig and MakeDnaSeqSingleExperimentNextflowConfig - Remove taxonId param and DB lookup from MakeDnaSeqNextflowConfig (no longer needed by dnaseq-nextflow pipeline) - Move retrieveGeneCNVAndPloidyQueries from snpAndCnvDNASeq to dnaseq template (organism-level files created once; symlinked into each experiment dir) - snpAndCnvDNASeq now handles processSingleExperiment only; load steps removed Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…ile and with new database schema
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Replaces dnaSeqExperimentFromAccession and dnaSeqExperimentFromLocal with a single dnaseqExperiment datasetTemplate modeled after longReadRnaSeqExperiment. Adds snpAndCnvDNASeq.xml workflow (processSingleExperiment + loadSingleExperiment via dnaseq-nextflow), MakeDnaSeqNextflowConfig.pm, and MakeDnaSeqLoadNextflowConfig.pm.