If git configured with SSH URL, running public repo fails with Auth fail

[melissachang]

Steps to reproduce the problem

Put into ~/.gitconfig:

[url "[email protected]:"]
        insteadOf = https://github.com/

Then running hello fails:

# Remove hello if it's already been downloaded
rm -rf ~/.nextflow/assets/nextflow-io/hello/

> nextflow run hello
N E X T F L O W  ~  version 21.10.6
Pulling nextflow-io/hello ...
[email protected]:nextflow-io/hello.git: Auth fail

Expected behavior and actual behavior

Expected: Running hello succeeds

Actual: Running hello fails

Program output

nextflow.log:

Mar-07 13:14:14.040 [main] INFO  nextflow.cli.CmdRun - Pulling nextflow-io/hello
 ...
Mar-07 13:14:14.041 [main] DEBUG nextflow.scm.RepositoryProvider - Request [cred
entials -:-] -> https://api.github.com/repos/nextflow-io/hello/contents/nextflow
.config
Mar-07 13:14:15.321 [main] DEBUG nextflow.scm.RepositoryProvider - Request [cred
entials -:-] -> https://api.github.com/repos/nextflow-io/hello/contents/main.nf
Mar-07 13:14:15.457 [main] DEBUG nextflow.scm.RepositoryProvider - Request [cred
entials -:-] -> https://api.github.com/repos/nextflow-io/hello
Mar-07 13:14:15.666 [main] DEBUG nextflow.scm.AssetManager - Pulling nextflow-io
/hello -- Using remote clone url: https://github.com/nextflow-io/hello.git
Mar-07 13:14:16.821 [main] INFO  nextflow.cli.CmdRun -  downloaded from https://
github.com/nextflow-io/hello.git
Mar-07 13:14:16.850 [main] INFO  nextflow.cli.CmdRun - Launching `nextflow-io/he
llo` [confident_mcclintock] - revision: ec11eb0ec7 [master]
Mar-07 13:14:16.862 [main] DEBUG nextflow.config.ConfigBuilder - Found config ba
desktop ~: rm !$
rm ~/.nextflow.log
desktop ~: rm -rf ~/.nextflow/assets/nextflow-io/hello/
desktop ~: vi ~/.gitconfig
desktop ~: nextflow run hello
N E X T F L O W  ~  version 21.10.6
Pulling nextflow-io/hello ...
[email protected]:nextflow-io/hello.git: Auth fail
desktop ~: m ~/.nextflow.log
Mar-07 13:15:18.226 [main] DEBUG nextflow.cli.Launcher - $> nextflow run hello
Mar-07 13:15:18.289 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  versi
on 21.10.6
Mar-07 13:15:18.310 [main] DEBUG nextflow.scm.AssetManager - Listing projects in
 folder: /usr/local/google/home/melchang/.nextflow/assets
Mar-07 13:15:18.320 [main] INFO  nextflow.cli.CmdRun - Pulling nextflow-io/hello
 ...
Mar-07 13:15:18.321 [main] DEBUG nextflow.scm.RepositoryProvider - Request [cred
entials -:-] -> https://api.github.com/repos/nextflow-io/hello/contents/nextflow
.config
Mar-07 13:15:19.546 [main] DEBUG nextflow.scm.RepositoryProvider - Request [cred
entials -:-] -> https://api.github.com/repos/nextflow-io/hello/contents/main.nf
Mar-07 13:15:19.680 [main] DEBUG nextflow.scm.RepositoryProvider - Request [cred
entials -:-] -> https://api.github.com/repos/nextflow-io/hello
Mar-07 13:15:19.889 [main] DEBUG nextflow.scm.AssetManager - Pulling nextflow-io
/hello -- Using remote clone url: https://github.com/nextflow-io/hello.git
Mar-07 13:15:21.087 [main] DEBUG nextflow.cli.Launcher - Operation aborted
org.eclipse.jgit.errors.TransportException: [email protected]:nextflow-io/hello.git
: Auth fail
	at org.eclipse.jgit.transport.JschConfigSessionFactory.getSession(JschCo
nfigSessionFactory.java:191)
	at org.eclipse.jgit.transport.SshTransport.getSession(SshTransport.java:
140)
	at org.eclipse.jgit.transport.TransportGitSsh$SshFetchConnection.<init>(
TransportGitSsh.java:280)
	at org.eclipse.jgit.transport.TransportGitSsh.openFetch(TransportGitSsh.
java:170)
	at org.eclipse.jgit.transport.FetchProcess.executeImp(FetchProcess.java:
138)
	at org.eclipse.jgit.transport.FetchProcess.execute(FetchProcess.java:124
)
	at org.eclipse.jgit.transport.Transport.fetch(Transport.java:1271)
	at org.eclipse.jgit.api.FetchCommand.call(FetchCommand.java:243)
	at org.eclipse.jgit.api.CloneCommand.fetch(CloneCommand.java:302)
	at org.eclipse.jgit.api.CloneCommand.call(CloneCommand.java:200)
	at nextflow.scm.AssetManager.download(AssetManager.groovy:608)
	at nextflow.scm.AssetManager.download(AssetManager.groovy)
	at nextflow.cli.CmdRun.getScriptFile(CmdRun.groovy:374)
	at nextflow.cli.CmdRun.run(CmdRun.groovy:264)
	at nextflow.cli.Launcher.run(Launcher.groovy:480)
	at nextflow.cli.Launcher.main(Launcher.groovy:639)
Caused by: com.jcraft.jsch.JSchException: Auth fail
	at com.jcraft.jsch.Session.connect(Session.java:519)
	at org.eclipse.jgit.transport.JschConfigSessionFactory.getSession(JschCo
nfigSessionFactory.java:145)
	... 15 common frames omitted

Environment

• Nextflow version: 21.10.6
• Java version: [?]
• Operating system: macOS
• Bash version: 5.1.8(1)

Context

My organization requires we clone git repos using ssh, that's why I have those lines in my .gitconfig.

[pditommaso]

SSH transport for Git is not supported