How evotools/nf-lo works
nf-LO is a Nextflow pipeline that turns source and target genome assemblies into UCSC liftOver-compatible chain files. Users provide FASTA inputs or identify assemblies for retrieval, select an aligner and distance preset, then run alignment and downstream processing. The repository separates acquisition, preprocessing, aligner-specific workflows, and postprocessing. The README documents these capabilities, but no source excerpts were provided, so implementation-level call ownership cannot be verified; uncertain module links are omitted or marked unverified.
Main entry points: main.nf nf-LO workflow · data.nf Genome acquisition · preprocess.nf Genome preprocessing · lastz.nf lastz alignment
Components 17
Genome inputs
- nf-LO workflow
main.nf - Genome acquisition
modules/subworkflows/data.nf - NCBI datasets
modules/processes/datasets/main.nf - iGenomes inputs
modules/processes/datasets/main.nf
Preparation
- Genome preprocessing
modules/subworkflows/preprocess.nf - Preprocess task
modules/processes/preprocess/main.nf
Genome alignment
- lastz alignment
modules/subworkflows/lastz.nf - lastz task
modules/processes/lastz/main.nf - BLAT alignment
modules/subworkflows/blat.nf - BLAT task
modules/processes/blat/main.nf - minimap2 alignment
modules/subworkflows/minimap2.nf - minimap2 task
modules/processes/minimap2/main.nf - GSAlign alignment
modules/subworkflows/GSAlign.nf - GSAlign task
modules/processes/GSAlign/main.nf
Chain output
- Chain generation
modules/subworkflows/liftover.nf - Alignment postprocess
modules/processes/postprocess/main.nf
Other components
- Pipeline user
Connections 16
- Pipeline user → nf-LO workflow: runs
README.md - nf-LO workflow → Genome acquisition: selects genomes
- Genome acquisition → NCBI datasets: retrieves assemblies
- Genome acquisition → iGenomes inputs: retrieves assemblies
- nf-LO workflow → Genome preprocessing: prepares genomes
- Genome preprocessing → Preprocess task: runs
- nf-LO workflow → lastz alignment: selects aligner
README.md - nf-LO workflow → BLAT alignment: selects aligner
README.md - nf-LO workflow → minimap2 alignment: selects aligner
README.md - nf-LO workflow → GSAlign alignment: selects aligner
README.md - lastz alignment → lastz task: runs
- BLAT alignment → BLAT task: runs
- minimap2 alignment → minimap2 task: runs
- GSAlign alignment → GSAlign task: runs
- nf-LO workflow → Chain generation: produces chain
README.md - Chain generation → Alignment postprocess: uses processing