Download fastq and fasta and run #104
Workflow file for this run
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| name: Test SARS-CoV-2 workflow | |
| on: [pull_request, workflow_dispatch] | |
| run-name: Download fastq and fasta and run | |
| 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 Cecret | |
| run: | | |
| docker --version | |
| mkdir reads | |
| wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR139/023/SRR13957123/SRR13957123_1.fastq.gz | |
| wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR139/023/SRR13957123/SRR13957123_2.fastq.gz | |
| mv *fastq.gz reads/. | |
| mkdir -p fastas | |
| wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123.consensus.fa | |
| mv SRR13957123.consensus.fa SRR13957123DB.fa | |
| mv *fa fastas/. | |
| nextflow run . -profile docker -c .github/workflows/github_actions.config --primer_set ncov_V3 --maxcpus 2 --medcpus 2 --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200 | |
| ls cecret* | |
| cat cecret*/cecret_results.txt | |
| - name: Clean | |
| run: rm -rf work .nextflow* |