Weird occassional error when running nf-core pipelines with bi profile

[apeltzer]

Examples are always like this:

Launching `nf-core/scrnaseq` [focused_einstein] - revision: ef3f49479f [dev]
NOTE: Your local project version looks outdated - a different revision is available in the remote repository [c8d04dc40a]
WARNING: Could not load nf-core/config profiles: https://raw.githubusercontent.com/nf-core/configs/master/nfcore_custom.config
No such file: Config file does not exist: https://raw.githubusercontent.com/nf-core/configs/master/conf/conf/igenomes.config

A hint what could go wrong is the second URL, that is of course not correct. I am a bit wondering what happens here and why this is duplicating the conf part of the URL.

@alexblaessle and I got hit by this a couple of times already

[apeltzer]

Further context for this issue:

Mar-15 14:44:16.548 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 21.10.6
Mar-15 14:44:17.524 [main] DEBUG nextflow.scm.AssetManager - Git config: /home//.nextflow/assets/nf-core/scrnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/scrnaseq.git
Mar-15 14:44:17.537 [main] DEBUG nextflow.scm.AssetManager - Git config: /home//.nextflow/assets/nf-core/scrnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/scrnaseq.git
Mar-15 14:44:17.934 [main] INFO  nextflow.cli.CmdRun - Launching `nf-core/scrnaseq` [serene_becquerel] - revision: ef3f49479f [dev]
Mar-15 14:44:18.375 [main] INFO  nextflow.scm.AssetManager - NOTE: Your local project version looks outdated - a different revision is available in the remote repository [c8d04dc40a]
Mar-15 14:44:18.392 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home//.nextflow/assets/nf-core/scrnaseq/nextflow.config
Mar-15 14:44:18.393 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home//.nextflow/assets/nf-core/scrnaseq/nextflow.config
Mar-15 14:44:18.402 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `bi,singularity`
Mar-15 14:44:18.605 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager
Mar-15 14:44:18.614 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Mar-15 14:44:18.615 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Mar-15 14:44:18.618 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Mar-15 14:44:18.621 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager
Mar-15 14:44:18.734 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager
Mar-15 14:44:18.734 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager
Mar-15 14:44:18.766 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager
Mar-15 14:44:18.766 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager
Mar-15 14:44:18.789 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager
Mar-15 14:44:18.986 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager
Mar-15 14:44:18.991 [main] ERROR nextflow.cli.Launcher - Unable to parse config file: '/home//.nextflow/assets/nf-core/scrnaseq/nextflow.config'

  Config file does not exist: https://raw.githubusercontent.com/nf-core/configs/master/conf/conf/igenomes.config

java.nio.file.NoSuchFileException: Config file does not exist: https://raw.githubusercontent.com/nf-core/configs/master/conf/conf/igenomes.config
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

I can run the nf-core/scrnaseq master branch, but whenever I try to doing this some DSL2 branch it breaks. Nextflow 21.10.6 is new enough so should be able to work with the DSL2 version in the branch.

[maxulysse]

@apeltzer still noticing this issue?

[apeltzer]

Nope, seems to be gone - will close