diff --git a/Pulumi.cape-cod-dev.yaml b/Pulumi.cape-cod-dev.yaml index 5a33bfc..b9f2ee8 100644 --- a/Pulumi.cape-cod-dev.yaml +++ b/Pulumi.cape-cod-dev.yaml @@ -1517,6 +1517,14 @@ config: value: "1" - type: MEMORY value: "2048" + mountPoints: + - sourceVolume: "nextflow_shared_data" + containerPath: "/mnt/nextflow_shared_data" + readOnly: true + volumes: + - name: "nextflow_shared_data" + efsVolumeConfiguration: + fileSystemId: fs-0cc7e588b5015c314 # `cape-cod:datalakehouse` (mapping, required) # Contains configuration specific to the data lake house (DLH). The DLH # contains tributaries, which are compionents that consist of a pair of raw diff --git a/assets/analysis-pipelines/bactopia/bactopia-base-3.2.0.json b/assets/analysis-pipelines/bactopia/bactopia-base-3.2.0.json index 1bf3cdd..b3fe260 100644 --- a/assets/analysis-pipelines/bactopia/bactopia-base-3.2.0.json +++ b/assets/analysis-pipelines/bactopia/bactopia-base-3.2.0.json @@ -12,6 +12,10 @@ "-profile": { "const": "aws", "default": "aws" + }, + "--aws_volumes": { + "const": "/opt/conda:/mnt/conda,/mnt/nextflow_shared_data:/mnt/nextflow_shared_data:ro", + "default": "/opt/conda:/mnt/conda,/mnt/nextflow_shared_data:/mnt/nextflow_shared_data:ro" } } }, diff --git a/assets/analysis-pipelines/bactopia/bactopia-base-dev.json b/assets/analysis-pipelines/bactopia/bactopia-base-dev.json index 3777c80..4b52ef6 100644 --- a/assets/analysis-pipelines/bactopia/bactopia-base-dev.json +++ b/assets/analysis-pipelines/bactopia/bactopia-base-dev.json @@ -12,6 +12,10 @@ "-profile": { "const": "aws", "default": "aws" + }, + "--aws_volumes": { + "const": "/opt/conda:/mnt/conda,/mnt/nextflow_shared_data:/mnt/nextflow_shared_data:ro", + "default": "/opt/conda:/mnt/conda,/mnt/nextflow_shared_data:/mnt/nextflow_shared_data:ro" } } }, diff --git a/assets/analysis-pipelines/bactopia/kraken2-bactopia-3.2.0.json b/assets/analysis-pipelines/bactopia/kraken2-bactopia-3.2.0.json index 23bf167..563db07 100644 --- a/assets/analysis-pipelines/bactopia/kraken2-bactopia-3.2.0.json +++ b/assets/analysis-pipelines/bactopia/kraken2-bactopia-3.2.0.json @@ -15,6 +15,11 @@ "const": "kraken2", "default": "kraken2" }, + "--kraken2_db": { + "type": "string", + "title": "Kraken2 Database Path", + "default": "/mnt/nextflow_shared_data/kraken2" + }, "--max_cpus": { "type": "integer", "title": "Max CPUs", diff --git a/assets/analysis-pipelines/bactopia/kraken2-bactopia-dev.json b/assets/analysis-pipelines/bactopia/kraken2-bactopia-dev.json index 10dd8c0..885c029 100644 --- a/assets/analysis-pipelines/bactopia/kraken2-bactopia-dev.json +++ b/assets/analysis-pipelines/bactopia/kraken2-bactopia-dev.json @@ -15,6 +15,11 @@ "const": "kraken2", "default": "kraken2" }, + "--kraken2_db": { + "type": "string", + "title": "Kraken2 Database Path", + "default": "/mnt/nextflow_shared_data/kraken2" + }, "--max_cpus": { "type": "integer", "title": "Max CPUs", diff --git a/assets/containers/nextflow-kickstart/entrypoint.sh b/assets/containers/nextflow-kickstart/entrypoint.sh index 1f6cf8a..190df90 100644 --- a/assets/containers/nextflow-kickstart/entrypoint.sh +++ b/assets/containers/nextflow-kickstart/entrypoint.sh @@ -46,6 +46,10 @@ cat >/nextflow.config <