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phylogenetic_workflow.yml
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name: Test Grandeur phylogenetic workflow
on: [pull_request, workflow_dispatch]
jobs:
test:
runs-on: ubuntu-20.04
steps:
- name: Checkout
uses: actions/checkout@v3
with:
lfs: true
- name: Checkout LFS objects
run: git lfs checkout
- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Run Grandeur
run: |
docker --version
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/904/864/595/GCA_904864595.1_INF333/GCA_904864595.1_INF333_genomic.fna.gz && gzip -d GCA_904864595.1_INF333_genomic.fna.gz
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/783/245/GCA_013783245.1_ASM1378324v1/GCA_013783245.1_ASM1378324v1_genomic.fna.gz && gzip -d GCA_013783245.1_ASM1378324v1_genomic.fna.gz
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/026/626/185/GCA_026626185.1_ASM2662618v1/GCA_026626185.1_ASM2662618v1_genomic.fna.gz && gzip -d GCA_026626185.1_ASM2662618v1_genomic.fna.gz
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/808/985/GCA_020808985.1_ASM2080898v1/GCA_020808985.1_ASM2080898v1_genomic.fna.gz && gzip -d GCA_020808985.1_ASM2080898v1_genomic.fna.gz
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/904/863/225/GCA_904863225.1_KSB1_6J/GCA_904863225.1_KSB1_6J_genomic.fna.gz && gzip -d GCA_904863225.1_KSB1_6J_genomic.fna.gz
mkdir fastas
mv *fna fastas/.
nextflow run . -profile docker --maxcpus 2 --medcpus 2
cat grandeur/grandeur_summary.tsv
nextflow run . -profile docker,msa --maxcpus 2 --medcpus 2 -resume
- name: Check MSA files
run: |
for file in grandeur/*/summary_statistics.txt grandeur/iqtree2/iqtree.treefile.nwk grandeur/snp-dists/snp_matrix.txt
do
head $file
wc -l $file
done