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Pipelines & AnalysisOverview

Pipelines & Analysis

SeqDesk integrates packaged Nextflow workflows for both study-scale analysis and order-scoped sequencing operations. Study pipelines run across complete studies, while order pipelines work on the linked sequencing files of individual order samples. SeqDesk generates the required inputs automatically and reports run progress in real time through weblog events.

Study vs Order PipelinesUnderstand when to use study pipelines, order pipelines, and what each scope writes back.Running a PipelineLaunch study-wide or order-scoped workflows from the correct SeqDesk context.Monitoring & DAG VisualizationWeblog events, DAG view, process progress, and real-time tracking.Available PipelinesStudy pipelines, order pipelines, and the current built-in package catalog.Adding Custom PipelinesManifest-first pipeline packaging: targets, writeback, samplesheet generation, and UI metadata.Results: Assemblies & BinsAssembly model, MAGs, completeness/contamination metrics, and artifacts.