ci_tests.yml

# This is a basic workflow to ensure the Bismark tools are working
name: Bismark CI workflow

# Controls when the action will run. Triggers the workflow on push or pull request events but only for the master branch
on: [push, pull_request]

# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
  # This workflow contains a single job called "BismarkCI"
  BismarkCI:
    # The type of runner that the job will run on
    runs-on: ubuntu-latest

    # Steps represent a sequence of tasks that will be executed as part of the job
    steps:
      - name: Check out Bismark source-code repository
        uses: actions/checkout@v2

      - name: Set up conda
        uses: conda-incubator/setup-miniconda@v2
        with:
          auto-update-conda: true
          python-version: 3.9

      - name: Install conda dependencies
        shell: bash -l {0}
        # Explanation for why we need to use shell: bash -l {0} is here: https://github.com/conda-incubator/setup-miniconda#important
        run: |
          conda config --add channels defaults
          conda config --add channels bioconda
          conda config --add channels conda-forge
          conda config --set channel_priority strict
          conda install "bowtie2>=2.4" hisat2 samtools

      - name: Bismark help message
        shell: bash -l {0}
        run: ./bismark --help

      - name: software versions
        shell: bash -l {0}
        run: |
          ./bismark --version
          samtools --version
          bowtie2 --version
          hisat2 --version

      - name: Genome Preparation
        shell: bash -l {0} # required: yes! see above
        run: |
          pwd
          ./bismark_genome_preparation --verbose ./test_files/
          ./bismark_genome_preparation --verbose --parallel 4 ./test_files/

      - name: Bismark PE run
        shell: bash -l {0}
        run: |
          ./bismark --genome ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
          ./deduplicate_bismark --bam test_R1_bismark_bt2_pe.bam
          ./bismark_methylation_extractor test_R1_bismark_bt2_pe.bam --gzip --CX --bed --genome ./test_files/
          ./bismark2report
          ./bismark2summary

      - name: Bismark SE run
        shell: bash -l {0}
        run: |
          ./bismark --genome ./test_files/ ./test_files/test_R1.fastq.gz
          ./deduplicate_bismark --bam test_R1_bismark_bt2.bam
          ./bismark_methylation_extractor test_R1_bismark_bt2.bam --gzip --CX --bed --genome ./test_files/

      - name: Bismark run with option ICPC
        shell: bash -l {0}
        run: |
          ./bismark --bowtie2 --icpc ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
          ./bismark --bowtie2 --icpc ./test_files/ ./test_files/test_R1.fastq.gz

      - name: Bismark run using HISAT2
        shell: bash -l {0}
        run: |
          ./bismark_genome_preparation --hisat2 --verbose ./test_files/
          ./bismark_genome_preparation --hisat2 --verbose --parallel 4 ./test_files/
          ./bismark --genome ./test_files/ --hisat2 ./test_files/test_R1.fastq.gz
          ./bismark --genome ./test_files/ --hisat2 -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
          ./deduplicate_bismark --bam test_R1_bismark_hisat2.bam
          ./bismark_methylation_extractor test_R1_bismark_hisat2.bam  --gzip --CX --bed --genome ./test_files/
          ./bismark_methylation_extractor test_R1_bismark_hisat2_pe.bam  --gzip --CX --bed --genome ./test_files/

      - name: Bismark run Multicore
        shell: bash -l {0}
        run: |
          ./bismark --genome ./test_files/ --parallel 4 -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
          ./bismark --genome ./test_files/ --hisat2 --parallel 4 -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
          ./bismark_methylation_extractor test_R1_bismark_bt2_pe.bam --gzip --CX --bed --parallel 8 --genome ./test_files/
          ./bismark_methylation_extractor test_R1_bismark_hisat2_pe.bam --gzip --CX --bed --parallel 8 --genome ./test_files/

      - name: coverage2cytosine
        shell: bash -l {0}
        run: |
          ./coverage2cytosine test_R1_bismark_bt2_pe.bismark.cov.gz --merge_CpG --genome ./test_files/ -o test.output
          ./coverage2cytosine test_R1_bismark_bt2_pe.bismark.cov.gz --NOMe-seq --genome ./test_files/ -o test.output

      - name: bam2nuc
        shell: bash -l {0}
        run: |
          ./bam2nuc --genome_folder ./test_files/ --genomic_composition_only
          ./bam2nuc --genome_folder ./test_files/ test_R1_bismark_bt2_pe.bam
          ./bam2nuc --genome_folder ./test_files/ test_R1_bismark_hisat2_pe.bam

      - name: Additional scenarios
        shell: bash -l {0}
        run: |
          ./bismark --pbat --genome ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
          ./bismark --non_directional --genome ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
          ./bismark --hisat2 --pbat --genome ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
          ./bismark --hisat2 --non_directional --genome ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz

      - name: bismark2bedGraph
        shell: bash -l {0}
        run: |
          ./bismark2bedGraph -o test.bedGraph --buffer 5G CpG_*
          ./bismark2bedGraph -o test.bedGraph --ucsc --buffer 5G CpG_*
          ./bismark2bedGraph -o test.bedGraph --CX --scaffolds CpG* CHG_* CHH_*
          ./bismark2bedGraph -o test.bedGraph --CX --ample_memory --zero_based CpG* CHH_* CHG_*

      - name: Filte non-conversion
        shell: bash -l {0}
        run: |
          ./filter_non_conversion test_R1_bismark_bt2_pe.bam
          ./filter_non_conversion --consecutive --threshold 6 test_R1_bismark_bt2.bam
          ./filter_non_conversion test_R1_bismark_hisat2_pe.bam
          ./filter_non_conversion --consecutive --threshold 6 test_R1_bismark_hisat2.bam
          ./filter_non_conversion --percentage_cutoff 66 --minimum_count 4 test_R1_bismark_bt2_pe.bam
          ./filter_non_conversion --percentage_cutoff 66 --minimum_count 4 test_R1_bismark_hisat2_pe.bam