Update 20231219 #63
Workflow file for this run
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| name: Test Grandeur 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 | |
| mkdir reads | |
| # lecleria genome - not an actual use-case | |
| wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR283/002/SRR2838702/SRR2838702_1.fastq.gz | |
| wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR283/002/SRR2838702/SRR2838702_2.fastq.gz | |
| mv *fastq.gz reads/. | |
| nextflow run . -profile docker --maxcpus 2 --medcpus 2 | |
| cat grandeur/grandeur_summary.tsv | |
| - name: Check summary files | |
| run: | | |
| for file in grandeur/mlst/mlst_summary.tsv | |
| do | |
| head $file | |
| wc -l $file | |
| done |