mirror of
https://github.com/MillironX/setup-nextflow.git
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style: Run prettier
This commit is contained in:
Edmund Miller
parent
9ec3bc304f
commit
147da60f8f
3 changed files with 104 additions and 108 deletions
20
action.yml
20
action.yml
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@ -1,22 +1,22 @@
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name: "Setup Nextflow"
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description: "Install Nextflow and add it to the PATH"
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author: "nf-core"
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name: 'Setup Nextflow'
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description: 'Install Nextflow and add it to the PATH'
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author: 'nf-core'
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inputs:
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version:
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description: "The Nextflow version to download (if necessary) and use. Example: 21.10.3"
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description: 'The Nextflow version to download (if necessary) and use. Example: 21.10.3'
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required: false
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default: "latest-stable"
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default: 'latest-stable'
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all:
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description: "Whether to install every Nextflow release via the '-all' distribution."
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required: false
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default: false
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token:
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description: "GitHub token to access the GitHub Releases API. The default token should be sufficient for all use cases."
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description: 'GitHub token to access the GitHub Releases API. The default token should be sufficient for all use cases.'
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required: false
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default: ${{ github.token }}
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runs:
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using: "node16"
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main: "dist/index.js"
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using: 'node16'
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main: 'dist/index.js'
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branding:
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icon: "shuffle"
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color: "green"
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icon: 'shuffle'
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color: 'green'
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176
index.ts
176
index.ts
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@ -1,180 +1,176 @@
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import * as core from "@actions/core";
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import * as exec from "@actions/exec";
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import * as fs from "fs";
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import * as github from "@actions/github";
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import * as tc from "@actions/tool-cache";
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import retry = require("async-retry");
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import semver = require("semver");
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import * as core from '@actions/core'
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import * as exec from '@actions/exec'
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import * as fs from 'fs'
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import * as github from '@actions/github'
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import * as tc from '@actions/tool-cache'
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import retry = require('async-retry')
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import semver = require('semver')
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const NEXTFLOW_REPO = { owner: "nextflow-io", repo: "nextflow" };
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const NEXTFLOW_REPO = {owner: 'nextflow-io', repo: 'nextflow'}
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async function all_nf_releases(ok) {
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return await ok.paginate(
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ok.rest.repos.listReleases,
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NEXTFLOW_REPO,
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(response) => response.data
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);
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response => response.data
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)
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}
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async function latest_stable_release_data(ok) {
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const { data: stable_release } = await ok.rest.repos.getLatestRelease(
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const {data: stable_release} = await ok.rest.repos.getLatestRelease(
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NEXTFLOW_REPO
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);
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)
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return stable_release;
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return stable_release
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}
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async function release_data(version, ok) {
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// Setup tag-based filtering
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let filter = (r) => {
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return semver.satisfies(r.tag_name, version, true);
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};
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let filter = r => {
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return semver.satisfies(r.tag_name, version, true)
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}
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// Check if the user passed a 'latest*' tag, and override filtering
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// accordingly
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if (version.includes("latest")) {
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if (version.includes("-everything")) {
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if (version.includes('latest')) {
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if (version.includes('-everything')) {
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// No filtering
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filter = (r) => {
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return true;
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};
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} else if (version.includes("-edge")) {
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filter = (r) => {
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return r.tag_name.endsWith("-edge");
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};
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filter = r => {
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return true
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}
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} else if (version.includes('-edge')) {
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filter = r => {
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return r.tag_name.endsWith('-edge')
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}
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} else {
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// This is special: passing 'latest' or 'latest-stable' allows us to use
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// the latest stable GitHub release direct from the API
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const stable_release = await latest_stable_release_data(ok);
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return stable_release;
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const stable_release = await latest_stable_release_data(ok)
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return stable_release
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}
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}
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// Get all the releases
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const all_releases = await all_nf_releases(ok);
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const all_releases = await all_nf_releases(ok)
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let matching_releases = all_releases.filter(filter);
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let matching_releases = all_releases.filter(filter)
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matching_releases.sort(function (x, y) {
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semver.compare(x.tag_name, y.tag_name, true);
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});
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semver.compare(x.tag_name, y.tag_name, true)
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})
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return matching_releases[0];
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return matching_releases[0]
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}
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function nextflow_bin_url(release, get_all) {
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const release_assets = release.assets;
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const all_asset = release_assets.filter((a) => {
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return a.browser_download_url.endsWith("-all");
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})[0];
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const regular_asset = release_assets.filter((a) => {
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return a.name == "nextflow";
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})[0];
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const release_assets = release.assets
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const all_asset = release_assets.filter(a => {
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return a.browser_download_url.endsWith('-all')
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})[0]
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const regular_asset = release_assets.filter(a => {
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return a.name == 'nextflow'
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})[0]
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const dl_asset = get_all ? all_asset : regular_asset;
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const dl_asset = get_all ? all_asset : regular_asset
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return dl_asset.browser_download_url;
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return dl_asset.browser_download_url
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}
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async function install_nextflow(url, version) {
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core.debug(`Downloading Nextflow from ${url}`);
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core.debug(`Downloading Nextflow from ${url}`)
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const nf_dl_path = await retry(
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async (bail) => {
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return await tc.downloadTool(url);
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async bail => {
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return await tc.downloadTool(url)
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},
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{
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onRetry: (err) => {
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core.debug(`Download of ${url} failed, trying again. Error ${err}`);
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},
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onRetry: err => {
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core.debug(`Download of ${url} failed, trying again. Error ${err}`)
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}
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}
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);
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)
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const temp_install_dir = fs.mkdtempSync(`nxf-${version}`);
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const nf_path = `${temp_install_dir}/nextflow`;
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const temp_install_dir = fs.mkdtempSync(`nxf-${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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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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return temp_install_dir
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}
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async function run() {
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// Set environment variables
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core.exportVariable("CAPSULE_LOG", "none");
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core.exportVariable('CAPSULE_LOG', 'none')
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// Read in the arguments
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const token = core.getInput("token");
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const version = core.getInput("version");
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const get_all = core.getBooleanInput("all");
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const token = core.getInput('token')
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const version = core.getInput('version')
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const get_all = core.getBooleanInput('all')
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let resolved_version = "";
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let resolved_version = ''
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// Setup the API
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let octokit = {};
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let octokit = {}
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try {
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octokit = github.getOctokit(token);
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octokit = github.getOctokit(token)
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} catch (e: any) {
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core.setFailed(
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`Could not authenticate to GitHub Releases API with provided token\n${e.message}`
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);
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)
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}
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// Get the release info for the desired release
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let release: any = {};
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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(
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`Input version '${version}' resolved to Nextflow ${release.name}`
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);
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release = await release_data(version, octokit)
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resolved_version = release.tag_name
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core.info(`Input version '${version}' resolved to Nextflow ${release.name}`)
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} catch (e: any) {
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core.setFailed(
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`Could not retrieve Nextflow release matching ${version}.\n${e.message}`
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);
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)
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}
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// Get the download url for the desired release
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let url = "";
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let url = ''
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try {
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url = nextflow_bin_url(release, get_all);
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core.info(`Preparing to download from ${url}`);
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url = nextflow_bin_url(release, get_all)
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core.info(`Preparing to download from ${url}`)
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} catch (e: any) {
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core.setFailed(`Could not parse the download URL\n${e.message}`);
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core.setFailed(`Could not parse the download URL\n${e.message}`)
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}
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try {
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// Download Nextflow and add it to path
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let nf_path = "";
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nf_path = tc.find("nextflow", resolved_version);
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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`);
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const nf_install_path = await install_nextflow(url, resolved_version);
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core.debug(`Could not find Nextflow ${resolved_version} in cache`)
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const nf_install_path = await install_nextflow(url, resolved_version)
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nf_path = await tc.cacheDir(
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nf_install_path,
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"nextflow",
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resolved_version
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);
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core.debug(`Added Nextflow to cache: ${nf_path}`);
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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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fs.rmdirSync(nf_install_path, {recursive: true})
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} else {
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core.debug(`Using cached version of Nextflow: ${nf_path}`);
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core.debug(`Using cached version of Nextflow: ${nf_path}`)
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}
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core.addPath(nf_path);
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core.addPath(nf_path)
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core.info(`Downloaded \`nextflow\` to ${nf_path} and added to PATH`);
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core.info(`Downloaded \`nextflow\` to ${nf_path} and added to PATH`)
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} catch (e: any) {
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core.setFailed(e.message);
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core.setFailed(e.message)
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}
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// Run Nextflow so it downloads its dependencies
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try {
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const nf_exit_code = await exec.exec("nextflow", ["help"])
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const nf_exit_code = await exec.exec('nextflow', ['help'])
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} 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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core.warning(
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'Nextflow appears to have installed correctly, but an error was thrown while running it.'
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)
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}
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}
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run();
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run()
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@ -1,10 +1,10 @@
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{
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"extends": "@tsconfig/node16/tsconfig.json",
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"compilerOptions": {
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"target": "es6",
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"module": "commonjs",
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"strict": true,
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"noImplicitAny": false,
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"esModuleInterop": true,
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}
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"extends": "@tsconfig/node16/tsconfig.json",
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"compilerOptions": {
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"target": "es6",
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"module": "commonjs",
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"strict": true,
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"noImplicitAny": false,
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"esModuleInterop": true
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}
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}
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