Update 20240520 #83
Workflow file for this run
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| name: Test Grandeur workflow with salmonella | |
| on: [pull_request, workflow_dispatch] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| nextflow -version | |
| - name: Run Grandeur | |
| run: | | |
| docker --version | |
| mkdir fastas | |
| for accession in GCA_019710395.3_ASM1971039v3 GCA_001652385.2_ASM165238v2 GCA_013344545.1_ASM1334454v1 | |
| do | |
| all=$(echo $accession | cut -f 2 -d "_") | |
| fir=$(echo $all | cut -c 1-3) | |
| mid=$(echo $all | cut -c 4-6) | |
| end=$(echo $all | cut -c 7-9) | |
| wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/$fir/$mid/$end/$accession/${accession}_genomic.fna.gz | |
| gzip -d ${accession}_genomic.fna.gz | |
| mv ${accession}_genomic.fna fastas/. | |
| done | |
| ls fastas/* > fastas.txt | |
| nextflow run . -profile docker -c .github/workflows/github_actions.config --fasta_list fastas.txt | |
| cat grandeur/grandeur_summary.tsv | |
| cat grandeur/summary/software_versions.yml | |
| ls grandeur/multiqc/multiqc_report.html | |
| - name: Check Salmonella file | |
| run: | | |
| for file in grandeur/seqsero2/seqsero2_results.txt | |
| do | |
| head $file | |
| wc -l $file | |
| done | |