Install and configure Apptainer

roles/apptainer/README.md

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+# 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

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+---
+
+apptainer_deb_repository: "ppa:apptainer/ppa"
+
+apptainer_deb_package: "apptainer=1.3.4*"
+
+apptainer_rpm_repository:
+
+apptainer_rpm_package: "apptainer-1.3.6"
+
+# e.g.
+#  - directive: "mount tmp"
+#    value: "no"
+apptainer_config_overrides: []

roles/apptainer/tasks/configure.yml

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+---
+
+- name: Override Apptainer config directives
+  command:
+    cmd: apptainer config global --set "{{ item.directive }}" "{{ item.value }}"
+  become: true
+  loop: "{{ apptainer_config_overrides }}"
+  loop_control:
+    label: "{{ item.directive }} = {{ item.value }}"

roles/apptainer/tasks/install.yml

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+---
+
+- name: Configure repository for Apptainer packages [deb]
+  apt_repository:
+    repo: "{{ apptainer_deb_repository }}"
+    update_cache: true
+  become: true
+  when: ansible_os_family == 'Debian'
+
+- name: Install Apptainer packages [deb]
+  apt:
+    name: "{{ apptainer_deb_package }}"
+    state: present
+    allow_downgrade: yes
+  become: true
+  when: ansible_os_family == 'Debian'
+
+- name: Configure repository for Apptainer packages [rpm]
+  yum_repository:
+      name: "{{ apptainer_rpm_repository.name }}"
+      description: >-
+        "{% if 'description' in apptainer_rpm_repository %}
+        {{ apptainer_rpm_repository.description }}
+        {% else %}
+        {{ apptainer_rpm_repository.name }} repository
+        {% endif %}"
+      baseurl: "{{ apptainer_rpm_repository.baseurl | default(omit)}}"
+      file: "{{ apptainer_rpm_repository.file | default(omit)}}"
+      gpgkey: "{{ apptainer_rpm_repository.gpgkey | default(omit)}}"
+      gpgcheck: "{{ apptainer_rpm_repository.gpgcheck | default(omit)}}"
+      cost: "{{ apptainer_rpm_repository.cost | default(omit)}}"
+      enabled: "{{ apptainer_rpm_repository.enabled | default(omit)}}"
+      exclude: "{{ apptainer_rpm_repository.exclude | default(omit)}}"
+      gpgcakey: "{{ apptainer_rpm_repository.gpgcakey | default(omit)}}"
+      includepkgs: "{{ apptainer_rpm_repository.includepkgs | default(omit)}}"
+      metadata_expire: "{{ apptainer_rpm_repository.metadata_expire | default(omit)}}"
+      metalink: "{{ apptainer_rpm_repository.metalink | default(omit)}}"
+      mirrorlist: "{{ apptainer_rpm_repository.mirrorlist | default(omit)}}"
+      mirrorlist_expire: "{{ apptainer_rpm_repository.mirrorlist_expire | default(omit)}}"
+      password: "{{ apptainer_rpm_repository.password | default(omit) }}"
+      priority: "{{ apptainer_rpm_repository.priority | default(omit)}}"
+      proxy: "{{ apptainer_rpm_repository.proxy | default(omit)}}"
+      proxy_password: "{{ apptainer_rpm_repository.proxy_password | default(omit)}}"
+      proxy_username: "{{ apptainer_rpm_repository.proxy_username | default(omit)}}"
+      repo_gpgcheck: "{{ apptainer_rpm_repository.repo_gpgcheck | default(omit)}}"
+      sslverify: "{{ apptainer_rpm_repository.sslverify | default(omit)}}"
+      username: "{{ apptainer_rpm_repository.username | default(omit) }}"
+      state: "{{ apptainer_rpm_repository.state | default(omit)}}"
+  become: true
+  when: 
+    - ansible_os_family == 'RedHat'
+    - apptainer_rpm_repository
+
+- name: Install Apptainer packages [rpm]
+  dnf:
+    name: "{{ apptainer_rpm_package }}"
+  become: true
+  when: ansible_os_family == 'RedHat'

roles/apptainer/tasks/main.yml

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+---
+
+- name: Install Apptainer
+  include_tasks: install.yml
+
+- name: Configure Apptainer
+  import_tasks: configure.yml

roles/nextflow/README.md

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+# nextflow
+
+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

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+---
+
+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

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+---
+
+- 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

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+---
+
+- 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

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+---
+
+- name: Install Nextflow
+  include_tasks: install.yml
+
+- name: Configure Nextflow
+  import_tasks: configure.yml