Add Nextflow role

roles/apptainer/README.md

@@ -0,0 +1,13 @@
+# apptainer
+
+Install and configure Apptainer on RedHat and Debian systems.
+
+## Usage
+
+| Name | Description | Default |
+| ---- | ----------- | ------- |
+|`apptainer_deb_repository` | DEB repository to install Apptainer from | "ppa:apptainer/ppa" |
+|`apptainer_deb_package` | Apptainer DEB package to install | "apptainer=1.3.4*" |
+|`apptainer_rpm_repository` | RPM repository to install Apptainer from | UNSET |
+|`apptainer_rpm_package` | Apptainer RPM package to install | "apptainer=1.3.6" |
+|`apptainer_config_overrides` | Configuration overrides to apply to Apptainer config| `[]` |

roles/apptainer/defaults/main.yml

@@ -8,4 +8,7 @@ apptainer_rpm_repository:
 
 apptainer_rpm_package: "apptainer-1.3.6"
 
-apptainer_config_overrides:
+# e.g.
+#  - "directive": "mount tmp"
+#    "value": "no"
+apptainer_config_overrides: []

roles/apptainer/tasks/configure.yml

@@ -4,7 +4,6 @@
   command:
     cmd: apptainer config global --set "{{ item.directive }}" "{{ item.value }}"
   become: true
-  when: apptainer_config_overrides
   loop: apptainer_config_overrides
   loop_control:
     label: "{{ item.directive }} = {{ item.value }}"

roles/nextflow/README.md

@@ -0,0 +1,12 @@
+# apptainer
+
+Install and configure Nextflow on RedHat and Debian systems.
+
+## Usage
+
+| Name | Description | Default |
+| ---- | ----------- | ------- |
+|`nextflow_openjdk_package_name` | Name of a package that provides Java JDK > 11 | "java-21-openjdk" or "openjdk-21-jdk" |
+|`nextflow_version` | Nextflow version to install | "v24.10.4" |
+|`nextflow_executable_url` | URL to download Nextflow from | https://github.com/nextflow-io/nextflow/releases/download/{{ nextflow_version }}/nextflow |
+|`nextflow_skel_config` | Config to add to /etc/skel/.nextflow/config | UNSET |

roles/nextflow/defaults/main.yml

@@ -0,0 +1,14 @@
+---
+
+nextflow_openjdk_package_name: >-
+  {{ 
+    'java-21-openjdk' 
+    if ansible_os_family == 'RedHat'
+    else 'openjdk-21-jdk'
+    }}
+
+nextflow_version: "v24.10.4"
+
+nextflow_executable_url: https://github.com/nextflow-io/nextflow/releases/download/{{ nextflow_version }}/nextflow
+
+nextflow_skel_config:

roles/nextflow/tasks/configure.yml

@@ -0,0 +1,15 @@
+---
+
+- name: Create Nextflow config directory in /etc/skel
+  file:
+    state: directory
+    path: /etc/skel/.nextflow
+  when: nextflow_skel_config
+  become: true
+
+- name: Write Nextflow config file to /etc/skel
+  copy:
+    dest: /etc/skel/.nextflow/config
+    content: "{{ nextflow_skel_config }}"
+  become: true
+  when: nextflow_skel_config

roles/nextflow/tasks/install.yml

@@ -0,0 +1,13 @@
+---
+
+- name: Install OpenJDK
+  package:
+    name: "{{ nextflow_openjdk_package_name }}"
+  become: true
+
+- name: Install Nextflow
+  get_url:
+    url: "{{ nextflow_executable_url }}"
+    dest: /usr/local/bin/nextflow
+    mode: u=rwx,g=rx,o=rx
+  become: true

roles/nextflow/tasks/main.yml

@@ -0,0 +1,7 @@
+---
+
+- name: Install Nextflow
+  include_tasks: install.yml
+
+- name: Configure Nextflow
+  import_tasks: configure.yml