SamplePrep alignment workflow
SamplePrepPipeline takes paired FASTQs through download, one align path, alignment QC, optional cfDNA fragmentomics, methylation extraction, extraction QC, archive, and cleanup.
ApplicationreadyLicense: MIT
GoliathOmics
Genomics workflows on GoliathApp: sample alignment, QC, and process packs.
GoliathOmics specializes the GoliathApp platform for genomics. A SamplePrep instance aligns each sample, runs alignment QC and extraction QC against the baked configuration window plus any per-sample overlay, and leaves methylation matrices for later study steps. Process packs choose an analyte, a library technique, and a disease or trait cohort on the methylation, RNA-seq, or proteomics modality. Read alignment and methylation calling are the standalone utilities GoliathAlign and MethylExtractor.
Features
Four align paths
Linear Clara Parabricks and GoliathAlign share sample.parabricks_fq2bam and switch on actionConfig.parabricks.engine. Stock pangenome uses sample.parabricks_giraffe. WGBS pangenome uses sample.methylgrapher_wgbs_align.
BAM stays on one worker
Align through sample.delete_bam is pinned with require_previous_worker. The BAM and staged FASTQs live on that worker's local scratch (METHYL_LOCAL_TMP), and delete_bam removes them there.
QC windows with per-sample overlays
Alignment QC and extraction QC both honor the resolvedConfig window baked at instance start. A sample may overlay alignment core_guardrails or extraction guardrails on top of that window.
Workflow JSON compiled into database nodes
DomainProgram JSON is compiled to a workflow definition and stored as database nodes. Starting an instance runs finalize_instance_context before the instance is created.
Process packs
Analyte, assay-procedure, and application packs cover analytes, library techniques, and disease or trait studies for methylation, RNA-seq, and proteomics.
Release profiles and worker enrollment
A version tag builds the MethylPipeline archive, assemble publishes the GoliathOmics bundle, and deploy applies a target profile or promotes on the runner. Workers enroll through the gateway REST API.
Depends on
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Used by
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Generated at build time from Goliath-Research/GoliathOmics@main/.goliath/product.json, validated with that repository’s .goliath/product.schema.json (schemaVersion 1).