Commit 3df49e15 authored by Devin OKelly's avatar Devin OKelly
Browse files

Fix to defaults so that singularity is in the biohpc.config as the default,...

Fix to defaults so that singularity is in the biohpc.config as the default, and endpoints for container pulls are in the appropriate repo
parent 6fc92794
Pipeline #10474 failed with stages
in 2 minutes and 6 seconds
......@@ -20,6 +20,10 @@ The workflow `workflow/main.nf` has three processes:
There is a single parameter `story`. This provides 1 or more files that the
workflow should run on.
## Containers
The default configuration for this workflow is located in ./workflow/configs/biohpc.config . This configuration will cause the Nextflow command to use the singularity executor for the uppercase, toLines, and wordcount processes, using Docker.io endpoints. The biohpc_*_gitlab.config files show how to instead use images pulled from a specified GitLab repository.
## Questions
If you have any questions about this workflow example, or Astrocyte in general,
......
......@@ -6,4 +6,13 @@ singularity {
process {
executor = 'local'
withName:uppercase {
container = 'ubuntu:latest'
}
withName:tolines {
container = 'ubuntu:latest'
}
withName:wordcounts {
container = 'centos:centos8'
}
}
......@@ -7,12 +7,12 @@ docker {
process {
executor = 'local'
withName:uppercase {
container = 'git.biohpc.swmed.edu:5050/s190450/astrocyte_example_wordcount/ubuntu:latest'
container = 'git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/ubuntu:latest'
}
withName:tolines {
container = 'git.biohpc.swmed.edu:5050/s190450/astrocyte_example_wordcount/ubuntu:latest'
container = 'git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/ubuntu:latest'
}
withName:wordcounts {
container = 'git.biohpc.swmed.edu:5050/s190450/astrocyte_example_wordcount/centos:centos8'
container = 'git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/centos:centos8'
}
}
singularity {
enabled = true
runOptions = '--bind /vagrant:/vagrant'
cacheDir = "$baseDir/images/singularity"
}
process {
executor = 'local'
withName:uppercase {
container = 'ubuntu:latest'
}
withName:tolines {
container = 'ubuntu:latest'
}
withName:wordcounts {
container = 'centos:centos8'
}
}
......@@ -8,15 +8,15 @@ singularity {
process {
executor = 'local'
withName:parameters {
container = 'git.biohpc.swmed.edu:5050/s190450/astrocyte_example_wordcount/ubuntu:latest'
container = 'git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/ubuntu:latest'
}
withName:uppercase {
container = 'docker://git.biohpc.swmed.edu:5050/s190450/astrocyte_example_wordcount/ubuntu:latest'
container = 'docker://git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/ubuntu:latest'
}
withName:tolines {
container = 'docker://git.biohpc.swmed.edu:5050/s190450/astrocyte_example_wordcount/ubuntu:latest'
container = 'docker://git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/ubuntu:latest'
}
withName:wordcounts {
container = 'docker://git.biohpc.swmed.edu:5050/s190450/astrocyte_example_wordcount/centos:centos8'
container = 'docker://git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/centos:centos8'
}
}
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