pixi.toml

[project]
name = "Swedish Earth Biogenome Project Assembly Pipeline"
version = "0.1.0"
description = "A de novo genome assembly pipeline"
authors = ["Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>"]
channels = ["conda-forge", "bioconda"]
platforms = ["linux-64", "osx-64", "osx-arm64"]

[tasks]
# Run Nextflow directly
test-docker = "nextflow run main.nf -profile docker,test"
test-singularity = "nextflow run main.nf -profile singularity,test"
dev = "nextflow run main.nf -profile docker,test,debug"
# Run nf-tests
nftest-docker = "nf-test test tests/main.nf.test"
nftest-singularity = "nf-test test tests/main.nf.test --profile singularity"
# Clean up
clean-work = "nextflow clean -f -before $(nextflow log -q | tail -n 1) && find work/ -type d -empty -delete"
clean-nf = "rm -rf .nextflow* work/"
clean-results = "rm -rf results/"
clean-nftest = "rm -rf .nf-test/"
clean-all = { depends-on = [ "clean-nf", "clean-results", "clean-nftest" ] }

[dependencies]
nextflow = ">=24.4.4,<24.5"
mamba = ">=1.5.10,<1.6"
nf-core = ">=3.0.2,<3.1"