biovat/pixi.toml at dev · NBISweden/biovat · GitHub

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[workspace]
name        = "biovat"
version     = "0.0.1"
description = "A pipeline for population genomics analysis of non-model organisms"
authors     = [
    "Verena Kutschera <verena.kutschera@nbis.se>",
    "Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>",
    "Cormac Kinsella <cormac.kinsella@nbis.se>",
    "André Soares <andre.soares@nbis.se>",
    "Jason Hill <jason.hill@nbis.se>",
    "Lorena Ament <lorena.ament@nbis.se>",
    "Per Unneberg <per.unneberg@nbis.se>",
    "Lucile Soler <lucile.soler@nbis.se>"
]
channels    = ["conda-forge", "bioconda"]
platforms   = ["linux-64", "osx-64", "osx-arm64"]

[dependencies]
nextflow    = ">=26.4.6,<27"
nf-core     = ">=4.0.3,<5"
nf-test     = ">=0.9.5,<0.10"
gh          = ">=2.97.0,<3"

[tasks.test-docker]
cmd         = "nextflow main.nf -profile docker,test -output-format none"
description = "Run the pipeline test profile with Docker"

[target.osx-arm64.tasks.test-docker]
cmd         = "nextflow main.nf -profile docker,arm64,test -output-format none"
description = "Run the pipeline test profile with Docker (arm64)"

[tasks.test-singularity]
cmd         = "nextflow main.nf -profile singularity,test -output-format none"
description = "Run the pipeline test profile with Singularity"

[tasks.test-conda]
cmd         = "nextflow main.nf -profile conda,test -output-format none"
description = "Run the pipeline test profile with Conda"

[tasks.help]
cmd         = "nextflow main.nf --help"
description = "Show the pipeline's command-line help"

[tasks.prune]
cmd         = "git fetch --prune && gh pr list --state merged --json headRefName -q '.[].headRefName' | xargs git branch -d 2>/dev/null || true"
description = "Delete local branches for PRs already merged on GitHub"

[tasks.pr-status]
cmd         = "gh pr checks"
description = "Show CI status of the pull request for the current branch"

[tasks.review-status]
cmd         = '''gh pr list --state open --json number,title,reviewDecision --jq '.[] | "\(.number)\t\(.reviewDecision)\t\(.title)"' '''
description = "Show review status for all open PRs"

[tasks.my-reviews]
cmd         = 'gh pr list --search "review-requested:@me"'
description = "List open PRs waiting on your review"

[tasks.my-issues]
cmd         = "gh issue list --assignee @me"
description = "List open issues assigned to you"

[tasks.pr-open]
cmd         = "gh pr view --web"
description = "Open the current branch's PR in the browser"

[tasks.format]
cmd         = "nextflow lint -format -harshil-alignment -spaces 4"
description = "Run Nextflow formatter on target file(s). Usage: <cmd> <file(s)>"

[tasks.lint-pipeline]
cmd         = "nf-core pipelines lint"
description = "Run the nf-core pipeline linter"

[tasks.lint-prek]
cmd         = "prek run --all-files --show-diff-on-failure --color=always"
description = "Run prek on all files"

[tasks.schema-build]
cmd         = "nf-core pipelines schema build"
description = "Build the pipeline schema"

[tasks.default-nf-test]
cmd         = "nf-test test tests/default.nf.test --profile +docker"
description = "Run the default nf-test profile with Docker"

[target.osx-arm64.tasks.default-nf-test]
cmd         = "nf-test test tests/default.nf.test --profile +docker,arm64"
description = "Run the default nf-test profile with Docker (arm64)"