Update 20231121 #43
Workflow file for this run
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| name: Test Grandeur workflow with Group A Strep | |
| 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 | |
| mkdir fastas | |
| for accession in GCA_001412635.1_ASM141263v1 GCA_016724885.1_ASM1672488v1 GCA_900475035.1_41965_F01 | |
| 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 | |
| nextflow run . -profile docker --maxcpus 2 --medcpus 2 | |
| cat grandeur/grandeur_summary.tsv | |
| - name: Check Strep pneumo file | |
| run: | | |
| for file in grandeur/emmtyper/emmtyper_summary.tsv | |
| do | |
| head $file | |
| wc -l $file | |
| done |