Skip to content

POC: Support pipeline archives instead of git repos or local paths #6093

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
wants to merge 1 commit into
base: master
Choose a base branch
from
Draft

POC: Support pipeline archives instead of git repos or local paths #6093

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
67 changes: 63 additions & 4 deletions modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -563,6 +563,61 @@ class CmdRun extends CmdBase implements HubOptions {
return new ScriptFile(file)
}

/*
* Handle archive URLs directly
*/
if (pipelineName.startsWith('http://') || pipelineName.startsWith('https://')) {
def url = pipelineName.toLowerCase()

if (url.endsWith('.zip') || url.endsWith('.tar.gz') || url.endsWith('.tgz')) {
log.info "Detected archive URL: $pipelineName"

// Use AssetManager to handle the archive
try {
// For direct invocation of archive URLs, we'll create a generic AssetManager
// and manually invoke its archive handling methods
def manager = new AssetManager()

// Create path in .nextflow/assets/artefacts directory
String pathPart = pipelineName.replaceFirst('^https?://', '')
pathPart = pathPart.replaceAll("[<>:\"|?*]", "_")
def artefactsRoot = new File(AssetManager.root, "artefacts")
File artefactPath = new File(artefactsRoot, pathPart)
artefactPath.parentFile.mkdirs()

if (!artefactPath.exists()) {
log.info "Downloading and extracting archive..."
// Download and extract the archive
manager.downloadAndExtractArchive(pipelineName, artefactPath)

log.debug "Downloaded and extracted to: $artefactPath"
}
else {
log.info "Using cached archive: $artefactPath"
}

// Check if the archive contains a single root directory (common for GitHub archives)
File[] files = artefactPath.listFiles()
if (files && files.length == 1 && files[0].isDirectory()) {
// The archive has a subdirectory - use that as the root
artefactPath = files[0]
log.debug "Using subdirectory as project root: $artefactPath"
}

// Now find the main script file in the extracted directory
File scriptFile = mainScript
? new File(artefactPath, mainScript)
: manager.setLocalPath(artefactPath).getMainScriptFile()

// Return the script as a local file
return new ScriptFile(scriptFile)
}
catch (Exception e) {
throw new AbortOperationException("Cannot download or extract archive: $pipelineName", e)
}
}
}

/*
* look for a file with the specified pipeline name
*/
Expand Down Expand Up @@ -595,11 +650,16 @@ class CmdRun extends CmdBase implements HubOptions {
}
// checkout requested revision
try {
manager.checkout(revision)
manager.updateModules()
// Only perform checkout if this is a Git repository (not archive-based)
if (!manager.isLocalArchiveRepo()) {
manager.checkout(revision)
manager.updateModules()
}
final scriptFile = manager.getScriptFile(mainScript)
if( checkForUpdate && !offline )
// Only check remote status for Git repositories
if (checkForUpdate && !offline && !manager.isLocalArchiveRepo()) {
manager.checkRemoteStatus(scriptFile.revisionInfo)
}
// return the script file
return scriptFile
}
Expand All @@ -609,7 +669,6 @@ class CmdRun extends CmdBase implements HubOptions {
catch( Exception e ) {
throw new AbortOperationException("Unknown error accessing project `$repo` -- Repository may be corrupted: ${manager.localPath}", e)
}

}

static protected File tryReadFromStdin() {
Expand Down
Loading
Loading