clean

At a glance

Repository: atlasxomics/clean · Display name: clean · Modality: Epigenomics · Stage: Helper Workflow

Overview

A Workflow for remediating microfluidic artifacts in spatial epigenomic data generated via DBiT-seq. Given the fragments and a Spatial folder, clean returns an artifact-free fragments.tsv.gz plus summary statistics.

It identifies outlier rows and columns whose fragment counts exceed a user-defined number of standard deviations above the mean row/column fragment count. Fragments in those outlier rows/columns are randomly downsampled to the average count, and the cleaned table is sorted into continuous chromosome blocks and bgzip-compressed. The result works directly with ArchR, Seurat, and other scATAC-seq packages.

Steps

1. cleaning_task — Detect outlier rows/columns (> deviations SD above the mean), downsample their tixels to the average fragment count, then sort and bgzip the cleaned fragments. Outputs are written under latch:///cleaned/<output_dir>/.

Internal step

An upload_registry_task writes the cleaned outputs to the Latch Registry (see Internal Tasks).

Inputs

Per Sample (samples: List[Sample]):

Field	Type	Description
run_id	str	Run identifier (ATX default Dxxxxx_NGxxxxx).
singlecell_file	LatchFile	singlecell.csv from preprocessing.
positions_file	LatchFile	tissue_positions_list.csv from the Spatial folder.
fragments_file	LatchFile	fragments.tsv.gz to clean.
output_dir	str	Output subdirectory under cleaned/.
deviations	int	Standard-deviation threshold for flagging outlier rows/columns.

Global: table_id — Registry table ID (internal upload; see note above).

Outputs

A CleaningOutput per sample — the run_id and a LatchDir under latch:///cleaned/<output_dir>/ containing:

cleaned/<output_dir>/
├── <fragments>.tsv.gz
├── <run_id>_cleaning_metrics.csv
└── singlecell.csv

File	Description
<fragments>.tsv.gz	The cleaned, sorted, bgzip-compressed fragments file (outlier tixels downsampled).
<run_id>_cleaning_metrics.csv	Cleaning summary — which rows/columns were flagged as outliers and the downsampling applied.
singlecell.csv	Per-barcode single-cell summary after cleaning.

Example run

(Representative LaunchPlan / batch-table example to be added.)