merge fastq

At a glance

Repository: atlasxomics/merge_fastq · Display name: merge fastq · Modality: Platform · Stage: Utility

Overview

A platform-agnostic Workflow for merging multiple FASTQ files — for example the same library sequenced across several lanes or from multiple providers — into a single file per read.

Input order matters

The order of input files must match between read 1 and read 2. If read 1 is ['novogene_R1.fastq', 'basespace_R1.fastq'], then read 2 must be ['novogene_R2.fastq', 'basespace_R2.fastq']. Run the Workflow once per read.

Steps

1. merge_task — Validates that all inputs share a consistent read ID and extension (test_reads / test_extensions), then concatenates them with cat into <run_id>_merged_R<read>.<ext> and uploads to latch:///merged/<output_dir>/.

Inputs

Parameter	Type	Description
run_id	str	ATX run ID; used as the merged-file prefix.
input_files	List[LatchFile]	FASTQ files to merge, in a consistent order across reads.
output_dir	str	Subdirectory name under merged/.

Outputs

A single merged LatchFile (<run_id>_merged_R<read>.<ext>) written to latch:///merged/<output_dir>/.

merged/<output_dir>/
└── <run_id>_merged_R<read>.<ext>

Example run

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