ATX impute

At a glance

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

Overview

A single-step Workflow for filling in missing lanes (rows or columns of tixels) in a spatial epigenomic experiment — for example when a microfluidic channel failed. Missing tixels are imputed from surrounding tixels, informed by a cluster specification, so the recovered grid can be carried into downstream analysis.

Steps

1. impute_task — Imputes the specified missing rows/columns in the fragments file using the tissue positions and cluster assignments, and writes the recovered fragments to the output directory.

Inputs

Parameter	Type	Description
run_id	str	ATX run ID (optional prefix).
missing_rows	List[int]	Rows to impute (1–50 or 1–96).
missing_columns	List[int]	Columns to impute (1–50 or 1–96).
fragments_file	LatchFile	fragments.tsv.gz from epigenomic preprocessing.
positions_file	LatchFile	tissue_positions_list.csv from the Spatial folder.
cluster_specification	LatchDir | LatchFile	ArchRProject or a CSV specifying each tixel's cluster.
output_directory	str	Output subdirectory name.

Outputs

A LatchDir under latch:///impute/<output_directory>/.

impute/<output_directory>/
├── imputed_<fragments>.tsv.gz
├── tissue_positions_list_clusters.csv
└── <run_id>_cleaning_metrics.csv

File	Description
imputed_<fragments>.tsv.gz	The imputed, re-sorted, bgzip-compressed fragments file — the missing lanes filled in.
tissue_positions_list_clusters.csv	Tissue positions annotated with the per-tixel cluster assignments used to guide imputation.
<run_id>_cleaning_metrics.csv	Summary metrics for the imputation.

Example run

LaunchPlan(
    impute_workflow,
    "default",
    {
        "run_id": "default",
        "missing_rows": [11],
        "missing_columns": [24],
        "fragments_file": LatchFile("latch:///fastq2frags/demo/chromap_output/fragments.tsv.gz"),
        "positions_file": LatchFile("latch:///spatials/demo/spatial/tissue_positions_list.csv"),
        "cluster_specification": LatchDir("latch:///epi_analysis_archr/demo/demo_ArchRProject"),
        "output_directory": "demo",
    },
)