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Closes #717. #200

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Closes #717.

Closes #717. #200

Workflow file for this run

.github/workflows/ci_tests.yml at 71148ce
# 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