setup-nextflow/index.ts

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import * as core from "@actions/core";
import * as exec from "@actions/exec";
import * as fs from "fs";
import * as github from "@actions/github";
import * as tc from "@actions/tool-cache";
import retry = require("async-retry");
import semver = require("semver");
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const NEXTFLOW_REPO = { owner: "nextflow-io", repo: "nextflow" };
async function all_nf_releases(ok) {
return await ok.paginate(
ok.rest.repos.listReleases,
NEXTFLOW_REPO,
(response) => response.data
);
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}
async function latest_stable_release_data(ok) {
const { data: stable_release } = await ok.rest.repos.getLatestRelease(
NEXTFLOW_REPO
);
return stable_release;
}
async function release_data(version, ok) {
// Setup tag-based filtering
let filter = (r) => {
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return semver.satisfies(r.tag_name, version, true);
};
// Check if the user passed a 'latest*' tag, and override filtering
// accordingly
if (version.includes("latest")) {
if (version.includes("-everything")) {
// No filtering
filter = (r) => {
return true;
};
} else if (version.includes("-edge")) {
filter = (r) => {
return r.tag_name.endsWith("-edge");
};
} else {
// This is special: passing 'latest' or 'latest-stable' allows us to use
// the latest stable GitHub release direct from the API
const stable_release = await latest_stable_release_data(ok);
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return stable_release;
}
}
// Get all the releases
const all_releases = await all_nf_releases(ok);
let matching_releases = all_releases.filter(filter);
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matching_releases.sort(function (x, y) {
semver.compare(x.tag_name, y.tag_name, true);
});
return matching_releases[0];
}
function nextflow_bin_url(release, get_all) {
const release_assets = release.assets;
const all_asset = release_assets.filter((a) => {
return a.browser_download_url.endsWith("-all");
})[0];
const regular_asset = release_assets.filter((a) => {
return a.name == "nextflow";
})[0];
const dl_asset = get_all ? all_asset : regular_asset;
return dl_asset.browser_download_url;
}
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async function install_nextflow(url, version) {
core.debug(`Downloading Nextflow from ${url}`);
const nf_dl_path = await retry(
async (bail) => {
return await tc.downloadTool(url);
},
{
onRetry: (err) => {
core.debug(`Download of ${url} failed, trying again. Error ${err}`);
},
}
);
const temp_install_dir = fs.mkdtempSync(`nxf-${version}`);
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const nf_path = `${temp_install_dir}/nextflow`;
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fs.renameSync(nf_dl_path, nf_path);
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fs.chmodSync(nf_path, "0711");
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return temp_install_dir;
}
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async function run() {
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// Set environment variables
core.exportVariable("CAPSULE_LOG", "none");
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// Read in the arguments
const token = core.getInput("token");
const version = core.getInput("version");
const get_all = core.getBooleanInput("all");
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let resolved_version = "";
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// Setup the API
let octokit = {};
try {
octokit = github.getOctokit(token);
} catch (e: any) {
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core.setFailed(
`Could not authenticate to GitHub Releases API with provided token\n${e.message}`
);
}
// Get the release info for the desired release
let release: any = {};
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try {
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release = await release_data(version, octokit);
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resolved_version = release.tag_name;
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core.info(
`Input version '${version}' resolved to Nextflow ${release.name}`
);
} catch (e: any) {
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core.setFailed(
`Could not retrieve Nextflow release matching ${version}.\n${e.message}`
);
}
// Get the download url for the desired release
let url = "";
try {
url = nextflow_bin_url(release, get_all);
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core.info(`Preparing to download from ${url}`);
} catch (e: any) {
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core.setFailed(`Could not parse the download URL\n${e.message}`);
}
try {
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// Download Nextflow and add it to path
let nf_path = "";
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nf_path = tc.find("nextflow", resolved_version);
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if (!nf_path) {
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core.debug(`Could not find Nextflow ${resolved_version} in cache`);
const nf_install_path = await install_nextflow(url, resolved_version);
nf_path = await tc.cacheDir(
nf_install_path,
"nextflow",
resolved_version
);
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core.debug(`Added Nextflow to cache: ${nf_path}`);
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fs.rmdirSync(nf_install_path, { recursive: true });
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} else {
core.debug(`Using cached version of Nextflow: ${nf_path}`);
}
core.addPath(nf_path);
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core.info(`Downloaded \`nextflow\` to ${nf_path} and added to PATH`);
} catch (e: any) {
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core.setFailed(e.message);
}
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// Run Nextflow so it downloads its dependencies
try {
const nf_exit_code = await exec.exec("nextflow", ["help"])
} catch (e: any) {
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core.warning("Nextflow appears to have installed correctly, but an error was thrown while running it.")
}
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}
run();