blat-nextflow

A Nextflow pipeline that aligns query sequences against a genome using BLAT (BLAST-Like Alignment Tool).

Overview

This pipeline is a Nextflow implementation of a BLAT-based sequence alignment step used in VEuPathDB's genomic data workflows. It splits an input genome FASTA into subsets, runs the UCSC blat aligner against a query FASTA for each subset, and merges the resulting PSL alignment records into a single output file. It is used within VEuPathDB's ReFlow-orchestrated pipelines wherever genomic sequences (or contigs) need to be aligned against a reference genome — for example, mapping assembled or query sequences onto a genome assembly.

Requirements

• Nextflow (DSL2)
• A container engine: Docker or Singularity/Apptainer

The pipeline runs the veupathdb/blat:1.1.0 container, which is built from the included Dockerfile and installs the UCSC blat binary via rsync from hgdownload.soe.ucsc.edu.

Execution profiles are provided under conf/:

• conf/docker.config — run with Docker (default, included via nextflow.config)
• conf/singularity.config — run with Singularity
• conf/lsf.config — run with Singularity on an LSF cluster

Usage

nextflow run VEuPathDB/blat-nextflow -r main -resume \
  --genomeFasta /path/to/genome.fa \
  --queryFasta  /path/to/query.fa \
  --outputDir   /path/to/results \
  -C conf/docker.config

The pipeline has a single, unnamed entry point (no -entry flag is needed). It:

1. Splits genomeFasta into subsets of fastaSubsetSize sequences each.
2. Runs blat for each subset against queryFasta.
3. Concatenates all resulting PSL records into one output file written to outputDir.

Key Parameters

Parameter	Default	Description
genomeFasta	data/genome.fa	Genome FASTA to split and search against (required).
queryFasta	data/nuc.fa	Query FASTA aligned against each genome subset (required).
fastaSubsetSize	1	Number of sequences per split of genomeFasta, controlling parallelism.
dbType	dna	BLAT database (target) sequence type: dna, prot, or dnax.
queryType	dna	BLAT query sequence type: dna, prot, dnax, or rnax.
outputDir	results	Directory the merged PSL output is published to.
outputFileName	output.psl	Name of the merged PSL output file.

Additional BLAT command-line options (e.g. -dots=10 -maxIntron=50) are set via process.withName:runBlat.ext.args in nextflow.config and can be overridden per deployment.

Output

A single PSL-format alignment file (outputDir/outputFileName, default results/output.psl) containing the concatenated BLAT alignment records for every genome subset searched against the query FASTA.