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main.yml
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# This is a basic workflow to Test HiCUP
name: HiCUP+ Test (Bowtie2)
# Controls when the action will run. Triggers the workflow on push or pull request
# events but only for the master branch
on:
push:
branches: [ master, devel, actions ]
pull_request:
branches: [ master, devel, actions ]
# 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 "build"
build:
# 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:
# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
- uses: actions/checkout@v2
# Runs a single command using the runners shell
- name: Run a one-line script
run: echo Hello, world!
# Runs a set of commands using the runners shell
- name: Update Ubuntu
run: |
sudo apt-get update
- name: Install dependencies
run: |
sudo apt install samtools
sudo apt install bowtie2
sudo apt install r-base-core
sudo apt install bioperl
- name: Test all perl scripts
run: |
$GITHUB_WORKSPACE/hicup --help
$GITHUB_WORKSPACE/hicup --version
$GITHUB_WORKSPACE/hicup_mapper --help
$GITHUB_WORKSPACE/hicup_digester --help
$GITHUB_WORKSPACE/hicup_truncater --help
$GITHUB_WORKSPACE/hicup_deduplicator 2>&1 | grep Please
$GITHUB_WORKSPACE/Conversion/hicup2hicpipe --help
$GITHUB_WORKSPACE/Conversion/hicup2gothic --help
$GITHUB_WORKSPACE/Conversion/hicup2fithic --help
$GITHUB_WORKSPACE/Conversion/hicup2homer --help
$GITHUB_WORKSPACE/Conversion/hicup2juicer --help
$GITHUB_WORKSPACE/Conversion/hicup2ncc --help
$GITHUB_WORKSPACE/Misc/find_common_fragment_interactions.pl --help || [[ $? == 255 ]]
$GITHUB_WORKSPACE/Misc/hicup_capture --help
$GITHUB_WORKSPACE/Misc/make_hic_array.pl || [[ $? == 255 ]]
$GITHUB_WORKSPACE/scribler/scribler --help
$GITHUB_WORKSPACE/scribler/scribl_capture_ditag_sorter.pl || [[ $? == 255 ]]
$GITHUB_WORKSPACE/scribler/scribl_capture.pl || [[ $? == 255 ]]
$GITHUB_WORKSPACE/scribler/scribl_capture_region_breakdown.pl || [[ $? == 255 ]]
- name: Download Test Dataset and FASTA files
run: |
wget -nv https://www.bioinformatics.babraham.ac.uk/projects/hicup/test_dataset.tar.gz
tar xvzf test_dataset.tar.gz
mkdir -p Homo_sapiens.GRCh38_Bowtie2_Index_HiCUP
cd Homo_sapiens.GRCh38_Bowtie2_Index_HiCUP
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes/Human/Homo_sapiens.GRCh38.1.bt2
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes/Human/Homo_sapiens.GRCh38.2.bt2
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes/Human/Homo_sapiens.GRCh38.3.bt2
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes/Human/Homo_sapiens.GRCh38.4.bt2
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes/Human/Homo_sapiens.GRCh38.rev.1.bt2
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes/Human/Homo_sapiens.GRCh38.rev.2.bt2
cd ..
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.2.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.3.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.4.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.5.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.6.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.7.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.8.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.9.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.10.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.11.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.12.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.13.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.14.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.15.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.16.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.17.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.18.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.19.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.20.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.22.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.MT.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.X.fa.gz
wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.Y.fa.gz
wget -nv https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr21.fa.gz
wget -nv https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr22.fa.gz
cat chr*.fa.gz | gunzip > chr21chr22_hg38.fa
- name: Build bowtie2 index
run: |
mkdir -p chr21chr22_hg38
bowtie2-build chr21chr22_hg38.fa chr21chr22_hg38/chr21chr22_hg38
- name: Run HiCUP
run: |
$GITHUB_WORKSPACE/hicup_digester --re1 A^AGCTT,HindIII --genome Human38chr21and22 --zip chr21chr22_hg38.fa
$GITHUB_WORKSPACE/hicup --bowtie2 $(which bowtie2) --digest Digest* --zip --threads 2 --index ./chr21chr22_hg38/chr21chr22_hg38 --shortest 50 --longest 700 test_dataset/*.fastq
- name: Check results
run: |
$GITHUB_WORKSPACE/Testing/hicup_checker --threshold 5 --expected $GITHUB_WORKSPACE/Testing/test_output/HiCUP_summary_report_lHWLvpbSoZ_13-54-49_16-02-2023.txt --new HiCUP_summary_report_*