diff --git a/README.md b/README.md index 4077ccb..89c8933 100644 --- a/README.md +++ b/README.md @@ -32,6 +32,14 @@ Configure your infrastructure using the appropriate configuration files listed i nf-canary adheres to the `--outdir` convention established by [nf-core](https://nf-co.re/) to determine the output file destination. If not specified, output files are written to the work directory under a subfolder named `outputs`. +### Overriding default container + +The container is specified by the `container` parameter, which defaults to `quay.io/biocontainers/ubuntu:24.04`. If you wish to use a different container, you can specify an alternative using the --container parameter. + +```nextflow +params.container = 'docker.io/ubuntu:24.04' +``` + ### Skipping Tests Skip individual tests by name using the `--skip` parameter, e.g., `--skip TEST_INPUT`. Multiple tests can be specified with comma-delimited values, e.g., `--skip TEST_CREATE_FILE,TEST_PASS_FILE`. The parameter is case-insensitive. diff --git a/nextflow.config b/nextflow.config index e7e4b34..8edb0c6 100644 --- a/nextflow.config +++ b/nextflow.config @@ -4,10 +4,11 @@ params { run = null outdir = null remoteFile = null + container = "quay.io/biocontainers/ubuntu:24.04" } process { - container = "docker.io/library/ubuntu:23.10" + container = params.container errorStrategy = "finish" when = { ( params.run ? params.run.split(',').any{ "NF_CANARY:${it.toUpperCase()}".contains(task.process) } : true ) && diff --git a/nextflow_schema.json b/nextflow_schema.json index 6e969fb..88668a4 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -27,6 +27,12 @@ "help_text": "Path to a remote file to use within the pipeline. This mimics a remote set of files such as reference data that may need to be retrieved prior to analysis. By default this is not specified and the test is not ran, add a remote file using standard Nextflow filenaming to pull a file from your storage (e.g. an S3 bucket or shared storage).", "format": "path" }, + "container": { + "type": "string", + "description": "Container URI for nf-canary", + "help_text": "Specifies the container URI. By default, this is an Ubuntu container on quay.io with no usage limits.", + "default": "quay.io/biocontainers/ubuntu:24.04" + }, "gpu": { "type": "boolean", "description": "Whether to test GPU utilization within a process."