Sample preparation tooling

GoliathOmics creates the sample directories and chooses the tool. GoliathAlign and MethylExtractor write only the directory the worker gives them. They do not import this product or GoliathApp. See Dependency direction.

Step	Tool	Where the bytes are written
FASTQ → BAM	Clara Parabricks fq2bam_meth, GoliathAlign on the same action (parabricks.engine=mojo), Clara giraffe, or methylGrapher	Worker-local {METHYL_LOCAL_TMP}/bam/{slug}-{digest}/{sample_id}.bam
Linear or stock-pangenome BAM → HDF5	MethylExtractor	Worker-local {METHYL_LOCAL_TMP}/extract/{slug}-{digest}/, then *.h5 and *.json published into sampleDir
WGBS pangenome calls	GoliathAlign MethylCall / MergeCpG	Same local extract directory, then *.h5 and *.json published into sampleDir

sampleDir is {sampleRoot}/align.{mode}.{engine}/ on the shared mount. The BAM stays on the align worker until sample.delete_bam. The pin and the four align paths are in Start a SamplePrep instance.

Operator matrix: alignment engines. Required tool features: omics-tool-requirements.md. Image bake: workers/docker/methylgrapher/README.md.

GOLIATH_ALIGN_ROOT points at the GoliathAlign checkout. MOJO_ALIGN_ROOT and the directory name mojo-align remain one-cycle aliases.