Refactoring #56
Workflow file for this run
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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 | |