I added a pipeline to Launchpad, using a private repo. I have added the right fine-grained GitHub credentials to the platform as well.
Aside from the basic features I set Main script
to segmentation.nf
(rather than the default main.nf
) and I’m using an aws
profile like (the repo nextflow.config
:
resume = true
tower {
enabled = true
}
docker {
enabled = true
runOptions = '--gpus all -u $(id -u):$(id -g)'
}
params {
input = null
pattern = ''
segs = 'fluid,aug'
}
process {
executor = 'local'
container = 'ghcr.io/phenopolis/image-analysis:latest'
withName: RUN_SEG {
maxForks = 4
}
}
profiles {
aws {
workDir = 's3://lairc-data-test/seqera/work'
params {
input = 's3://lairc-data-test/sample'
pattern = ''
segs = 'fluid'
}
process {
executor = 'awsbatch'
queue = 'TowerForge-28CYqnaN5bmBllepvCQYRB'
scratch = false
}
wave {
enabled = true
strategy = 'container'
}
fusion {
enabled = true
}
aws {
region = 'eu-west-2'
batch {
volumes = '/scratch/fusion:/tmp'
}
}
}
}
timeline {
enabled = true
file = "results/pipeline_info/execution_timeline.html"
}
report {
enabled = true
file = "results_/pipeline_info/execution_report.html"
}
trace {
enabled = true
file = "results/pipeline_info/pipeline_trace.txt"
}
dag {
enabled = true
overwrite = true
direction = 'TB'
verbose = true
file = "results/pipeline_info/pipeline_dag.html"
}
I’m am not adding any Pipeline parameters or Nextflow config file other than the one already in the repo. It’s a test and the input parameters are defined in the aws
profile and I’m using a S3 path for the file input.
When I launch my pipeline it fails with a cryptic error:
The workflow execution failed to start. Exit status: 1
Essential container in task exited
Nextflow 24.10.5 is available - Please consider updating your version to it
N E X T F L O W ~ version 24.10.4
Pulling phenopolis/segmentation-nf ...
Project config file is malformed -- Cause: Ambiguous method overloading for method java.io.File#<init>.
Cannot resolve which method to invoke for [null] due to overlapping prototypes between:
[class java.lang.String]
[class java.net.URI]
Then I edited my pipeline to add Revision number
→ main
(The fact that I am able to select aws
for profile and main
for revision reassures me that the Seqera platform is accessing my private repo through my credentials).
Then I run it again and got a different error:
The workflow execution failed to start. Exit status: 1
Essential container in task exited
Nextflow 24.10.5 is available - Please consider updating your version to it
N E X T F L O W ~ version 24.10.4
Pulling phenopolis/segmentation-nf ...
Remote resource not found: https://api.github.com/repos/phenopolis/segmentation-nf/contents/main.nf?ref=main
Which seems a bug for me, because I clearly specified segmentation.nf
instead of main.nf
.
Besides:
curl -H "Authorization: token my_github_token" \
-H "Accept: application/vnd.github.v3.raw" \
https://api.github.com/repos/phenopolis/segmentation-nf/contents/segmentation.nf?ref=main
does work as expect.
So, if anyone can help me to debug my issues, it’s very much appreciated.