docker-compose-git-all.yml

x-mira-nf-git-repo:
  &mira-nf-git-repo
  https://github.com/CDCgov/MIRA-NF.git#master

x-python-image:
  &python-image
  python:3.10-alpine

x-python-version:
  &python-version
  python3.10

x-pyarrow-image:
  &pyarrow-image
  mira-nf:pyarrow-alpine

x-mira-nf-image:
  &mira-nf-image
  mira-nf:python3.10-alpine

x-data-volume:
  &data-volume
  type: bind
  source: /home/snu3/Github/FLU_SC2_SEQUENCING
  target: /data

services:
  multiqc:
    container_name: multiqc
    image: mira-nf:multiqc-alpine
    build:
      context: *mira-nf-git-repo
      dockerfile: multiqc/Dockerfile-multiqc
      args:
        python_image: *python-image
        python_version: *python-version
        multiqc_version: 1.19
    restart: always
    volumes:
      - *data-volume
    command: tail -f /dev/null

  fastqc:
    container_name: fastqc
    image: mira-nf:fastqc-alpine
    build:
      context: *mira-nf-git-repo
      dockerfile: fastqc/Dockerfile-fastqc
      args:
        python_image: *python-image
        python_version: *python-version
        fastqc_version: 0.12.1
    restart: always
    volumes:
      - *data-volume
    command: tail -f /dev/null

  bbtools:
    container_name: bbtools
    image: mira-nf:bbtools-alpine
    build:
      context: *mira-nf-git-repo
      dockerfile: bbtools/Dockerfile-bbtools
      args:
        python_image: *python-image
        python_version: *python-version
    restart: always
    volumes:
      - *data-volume
    command: tail -f /dev/null

  pyarrow: 
    container_name: pyarrow
    image: *pyarrow-image
    build:
      context: *mira-nf-git-repo
      dockerfile: pyarrow/Dockerfile-pyarrow
      args:
        python_image: *python-image
        ARROW_VERSION: 17.0.0
    restart: always
    volumes:
      - *data-volume
    command: tail -f /dev/null

  cutadapt:
    container_name: cutadapt
    image: mira-nf:cutadapt-alpine
    build:
      context: *mira-nf-git-repo
      dockerfile: cutadapt/Dockerfile-cutadapt
      args:
        python_image: *pyarrow-image
        python_version: *python-version
        cutadapt_version: 4.4
    depends_on:
      - pyarrow
    restart: always
    volumes:
      - *data-volume
    command: tail -f /dev/null

  mira-nf: 
    container_name: mira-nf
    image: *mira-nf-image
    build:
      context: *mira-nf-git-repo
      dockerfile: Dockerfile
      args:
        python_image: *pyarrow-image
        python_version: *python-version
    depends_on:
      - multiqc
      - fastqc
      - bbtools
      - cutadapt
      - pyarrow
    restart: always
    volumes:
      - *data-volume
    command: tail -f /dev/null