├── .github └── workflows │ ├── CI-blat.yml │ ├── CI-gsa.yml │ ├── CI-lastz.yml │ ├── CI-mm2.yml │ ├── conda.yml │ ├── docker-publish.yml │ └── singularity.yml ├── .gitignore ├── CHANGELOG.md ├── Dockerfile ├── LICENSE ├── README.md ├── assets ├── HoxD55.q ├── environment.yml ├── gatherMetrics.Rmd ├── general.q ├── human_chimp.v2.q ├── install.sh ├── install_maftools.sh ├── maf-environment.yml └── r-environment.yml ├── conf ├── base.config ├── conda.config ├── eddie.config ├── eddie_conda.config ├── igenomes.config ├── params.config ├── test.config └── verysmall.config ├── data ├── GCF_001549955.1_ASM154995v1_genomic.fna ├── GCF_001549955.1_ASM154995v1_genomic.gff.gz └── GCF_011751205.1_ASM1175120v1_genomic.fna ├── docs ├── Makefile ├── alignments.md ├── chain.md ├── changelog.md ├── citations.md ├── conf.py ├── customconf.md ├── environment.yml ├── faq.md ├── index.rst ├── inputs.md ├── install.md ├── liftover.md ├── make.bat ├── notes.md ├── output.md ├── reports.md ├── requirements.txt ├── resources.md └── step.md ├── environment.yml ├── main.nf ├── modules ├── processes │ ├── GSAlign │ │ └── main.nf │ ├── blat │ │ └── main.nf │ ├── datasets │ │ └── main.nf │ ├── help │ │ └── main.nf │ ├── lastz │ │ └── main.nf │ ├── minimap2 │ │ └── main.nf │ ├── postprocess │ │ └── main.nf │ └── preprocess │ │ └── main.nf └── subworkflows │ ├── GSAlign.nf │ ├── blat.nf │ ├── data.nf │ ├── lastz.nf │ ├── liftover.nf │ ├── minimap2.nf │ └── preprocess.nf ├── nextflow.config ├── nextflow_schema.json └── singularity.def /.github/workflows/CI-blat.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/evotools/nf-LO/HEAD/.github/workflows/CI-blat.yml -------------------------------------------------------------------------------- /.github/workflows/CI-gsa.yml: -------------------------------------------------------------------------------- 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