dnaseq Experiment#83
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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
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Adds CopyDnaseqBigwigToWebSvc workflow step and wires it into snpAndCnvDNASeq.xml after processSingleExperimentOnCluster. Iterates per-sample subdirectories in resultsDirectory and copies .bw files to $websiteFilesDir/.../dnaseq/bigwig/$experimentDatasetName/$sampleName/. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Conflict resolutions: - runGeneCNVAndPloidyQuery: accepted master deletion - RetrieveGeneCNVAndPloidyQueries.pm: accepted master version - dnaseq.xml: kept HEAD (makeDataDir dependency for makeGeneFootprintFile; snpAndCnvDNASeq params intact — fromSRA/relativeWebServicesDir/geneSourceIdOrthologFile/ chrsForCalcsFile required by subgraph, master's fromBAM/isLocal not declared params) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…low config Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…results Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…versal hang Replaces deep glob traversal of the dnaseq tree with a Perl-based gather step that symlinks results files into flat staging subdirs before config generation, so PathVisitors only enumerate a small flat directory. Also fixes hardcoded /home/rdemko/ paths in MakeDnaSeqMergeExperimentsNextflowConfig. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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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.