diff --git a/.github/workflows/salmon_index.yml b/.github/workflows/salmon_index.yml new file mode 100644 index 00000000..e3b065e8 --- /dev/null +++ b/.github/workflows/salmon_index.yml @@ -0,0 +1,40 @@ +name: salmon_index +on: + push: + paths: + - software/salmon/index/** + - .github/workflows/salmon_index.yml + - tests/software/salmon/** + pull_request: + paths: + - software/salmon/index/** + - .github/workflows/salmon_index.yml + - tests/software/salmon/** + +jobs: + ci_test: + runs-on: ubuntu-latest + strategy: + matrix: + nxf_version: [20.11.0-edge] + env: + NXF_ANSI_LOG: false + steps: + - uses: actions/checkout@v2 + + - name: Install Nextflow + env: + NXF_VER: ${{ matrix.nxf_version }} + run: | + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ + + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: "3.x" + - name: Install dependencies + run: python -m pip install --upgrade pip pytest-workflow + + # Test the module + - run: pytest --tag salmon_index --symlink --wt 2 diff --git a/tests/software/salmon/test.yml b/tests/software/salmon/test.yml index 3c891557..ec8ef998 100644 --- a/tests/software/salmon/test.yml +++ b/tests/software/salmon/test.yml @@ -4,8 +4,6 @@ - salmon - salmon_index files: - - path: output/salmon/salmon/ref_indexing.log - md5sum: 712121a1bc50e7ef3e0c0f115886be13 - path: output/salmon/salmon/refseq.bin md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7 - path: output/salmon/salmon/versionInfo.json @@ -14,10 +12,6 @@ md5sum: f57562f1fca3ae7b133f895ae13c3d08 - path: output/salmon/salmon/mphf.bin md5sum: 53669a47610e33e031faafd32703b714 - - path: output/salmon/salmon/pre_indexing.log - md5sum: 542ae3f1088357c2f867fe56cc01ca5c - - path: output/salmon/salmon/ctable.bin - md5sum: 320ed80e82259e47bd178275889067c5 - path: output/salmon/salmon/duplicate_clusters.tsv md5sum: 51b5292e3a874119c0e1aa566e95d70c - path: output/salmon/salmon/reflengths.bin @@ -30,10 +24,6 @@ md5sum: 27a76542337df436436e66017f66dd25 - path: output/salmon/salmon/rank.bin md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71 - - path: output/salmon/salmon/pos.bin - md5sum: 23ba28cc5a2511cb1cd7ef6ed555d3f8 - - path: output/salmon/salmon/seq.bin - md5sum: 8750937e595a8e56e7bc9a9a7d600c44 - name: salmon quant paired end command: nextflow run ./tests/software/salmon -profile docker -entry test_salmon_quant_pe -c tests/config/nextflow.confi