diff --git a/.github/workflows/test_assembler_none.yml b/.github/workflows/test_assembler_none.yml new file mode 100755 index 0000000..edada46 --- /dev/null +++ b/.github/workflows/test_assembler_none.yml @@ -0,0 +1,40 @@ +name: Test Donut Falls no assemblers + +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/ + + - name: Download Unicycler test files + run: | + mkdir reads + # from unicycler test data + wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/short_reads_1.fastq.gz + wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/short_reads_2.fastq.gz + #wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/long_reads_high_depth.fastq.gz + wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/long_reads_low_depth.fastq.gz + + mv *fastq.gz reads/. + + - name: Run Donut Falls + run: | + docker --version + + nextflow run . -profile docker -c .github/workflows/github_actions.config --sample_sheet .github/workflows/github_actions_hybrid_sample_sheet.txt --assembler doesnt_exist + + tree donut_falls + + - name: Check files + run: | + ls donut_falls/multiqc/multiqc_report.html + cat donut_falls/summary/donut_falls_summary.json \ No newline at end of file