GC context file now have the threshold set to 1 as intended #173
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| # 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 |