test.yaml

name: Test Geneshot

on: [push, pull_request]  

jobs:

  preproccessing:
    runs-on: ubuntu-22.04
    env:
      NXF_ANSI_LOG: 0
    steps:
      - uses: actions/checkout@v1
      - name: Install Nextflow
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
      - name: Free disk space
        run: |
          sudo swapoff -a
          sudo rm -f /swapfile
          sudo apt clean
          docker rmi $(docker image ls -aq)
          df -h
      - name:  Run preprocess
        run: |
          NXF_VER=23.10.0 nextflow run modules/preprocess.nf --manifest data/mock.manifest.csv --output output --host_index data/hg_chr_21_bwa_index.tar.gz  -w work/  -with-docker ubuntu:22.04 -c nextflow.config.sample -profile testing
      - name:  Validate results 
        run: |
          tree output/
          [[ -s output/qc/manifest.qc.csv ]]
          [[ -s output/qc/Mock__11.R1.fastq.gz ]]
          [[ -s output/qc/Mock__13__R1.noadapt.nohuman.fq.gz ]]

  composition_metaphlan2:
    runs-on: ubuntu-22.04
    env:
      NXF_ANSI_LOG: 0
    steps:
      - uses: actions/checkout@v1
      - name: Install Nextflow
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
      - name: Free disk space
        run: |
          sudo swapoff -a
          sudo rm -f /swapfile
          sudo apt clean
          docker rmi $(docker image ls -aq)
          df -h
      - name:  Run geneshot
        run: |
          NXF_VER=23.10.0 nextflow run modules/composition.nf --manifest data/example_output/qc/manifest.qc.se.csv --output output -w work/  -with-docker ubuntu:22.04 -c nextflow.config.sample -profile testing
      - name:  Validate results 
        run: |
          tree output/
          [[ -s output/MetaPhlAn2/metaphlan2.results.csv.gz ]]
          [[ -s output/MetaPhlAn2/metaphlan2.species.h5ad ]]
          
  allele_catalog:
    runs-on: ubuntu-22.04
    env:
      NXF_ANSI_LOG: 0
    steps:
      - uses: actions/checkout@v1
      - name: Install Nextflow
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
      - name: Free disk space
        run: |
          sudo swapoff -a
          sudo rm -f /swapfile
          sudo apt clean
          docker rmi $(docker image ls -aq)
          df -h
      - name:  Run geneshot
        run: |
          NXF_VER=23.10.0 nextflow run modules/allele_catalog.nf --manifest data/example_output/qc/manifest.qc.csv --output output -w work/  -with-docker ubuntu:22.04 -c nextflow.config.sample -profile testing 
      - name:  Validate results 
        run: |
          tree output/
          [[ -s output/alleles/allele_info.csv.gz ]]
          [[ -s output/alleles/alleles.faa.gz ]]
          [[ -s output/alleles/alleles.faa.gz.dmnd ]]

  allele_clustering:
    runs-on: ubuntu-22.04
    env:
      NXF_ANSI_LOG: 0
    steps:
      - uses: actions/checkout@v1
      - name: Install Nextflow
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
      - name: Free disk space
        run: |
          sudo swapoff -a
          sudo rm -f /swapfile
          sudo apt clean
          docker rmi $(docker image ls -aq)
          df -h
      - name:  Run geneshot
        run: |
          NXF_VER=23.10.0 nextflow run modules/allele_clustering.nf --alleles data/example_output/alleles/alleles.faa.gz --allele_info data/example_output/alleles/allele_info.csv.gz --output output -w work/  -with-docker ubuntu:22.04 -c nextflow.config.sample -profile testing
      - name:  Validate results 
        run: |
          tree output/
          [[ -s output/alleles/Allele_Cluster_info.csv.gz ]]
          [[ -s output/alleles/centroids.C100.fastp.gz ]]
          [[ -s output/alleles/centroids.C90.fastp.gz ]]
          [[ -s output/alleles/centroids.C50.fastp.gz ]]
          [[ -s output/alleles/centroids.C100.fastp.gz.dmnd ]]
          [[ -s output/alleles/centroids.C90.fastp.gz.dmnd ]]
          [[ -s output/alleles/centroids.C50.fastp.gz.dmnd ]]

  allele_quantification:
    runs-on: ubuntu-22.04
    env:
      NXF_ANSI_LOG: 0
    steps:
      - uses: actions/checkout@v1
      - name: Install Nextflow
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
      - name: Free disk space
        run: |
          sudo swapoff -a
          sudo rm -f /swapfile
          sudo apt clean
          docker rmi $(docker image ls -aq)
          df -h
      - name:  Run geneshot
        run: |
          NXF_VER=23.10.0 nextflow run modules/quantify.nf --manifest data/example_output/qc/manifest.qc.csv --allele_fasta data/example_output/alleles/alleles.faa.gz  --output output -w work/  -with-docker ubuntu:22.04 -c nextflow.config.sample -profile testing
      - name:  Validate results 
        run: |
          tree output/
          [[ -s output/quantify/specimen_allele_quantity.h5ad ]]