fragment fixer

At a glance

Repository: atlasxomics/fragment_fixer · Display name: fragment fixer · Modality: Epigenomics · Stage: Helper Workflow

Overview

A single-step Workflow that screens alignment / fragment files for lines that fall outside the chromosome coordinates of a reference genome (out-of-bounds fragments that can break downstream tools) and emits a corrected file. Useful for salvaging Chromap output produced against a mismatched or older genome build.

Steps

1. ff_task — Screens the input BED / fragment file against the reference genome's chromosome sizes, removes out-of-bounds lines, and writes the corrected file (as fragments.tsv.gz or aln.bed) under latch:///ff_outs/<output_dir>/.

Inputs

Parameter	Type	Description
input_file	LatchFile	BED / BED-like file from Chromap or a similar aligner.
run_id	str	Text prepended to the output file name.
genome	enum	Reference genome: mm39, mm10, hg38, rnor6.
output_type	enum	Output format: fragments.tsv.gz or aln.bed.
output_dir	str	Output subdirectory under ff_outs/.

Outputs

A LatchDir under latch:///ff_outs/<output_dir>/ containing the corrected file:

ff_outs/<output_dir>/
└── <run_id>_ff_aln.bed          # or fragments.tsv.gz, per output_type

File	Description
<run_id>_ff_aln.bed or <run_id> fragments .tsv.gz	The screened, corrected alignment / fragments file — lines that fall outside the reference genome's chromosome coordinates are removed. The format (aln.bed vs fragments.tsv.gz) is set by output_type.

Example run

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