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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -22,10 +22,27 @@ jobs: | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}" | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| NXF_VER: | ||
| - "22.10.1" | ||
| - "latest-everything" | ||
| parameters: | ||
| - "--preprocessing_qc_tool falco" | ||
| - "--perform_longread_qc false" | ||
| - "--perform_shortread_qc false" | ||
| - "--shortread_qc_tool fastp" | ||
| - "--shortread_qc_tool fastp --shortread_qc_mergepairs --shortread_qc_includeunmerged" | ||
| - "--shortread_qc_tool fastp --shortread_qc_mergepairs" | ||
| - "--shortread_qc_tool adapterremoval" | ||
| - "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs --shortread_qc_includeunmerged" | ||
| - "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs" | ||
| - "--shortread_complexityfilter_tool bbduk" | ||
| - "--shortread_complexityfilter_tool prinseqplusplus" | ||
| - "--perform_runmerging" | ||
| - "--perform_runmerging --shortread_qc_mergepairs" | ||
| - "--shortread_complexityfilter false --perform_shortread_hostremoval" | ||
|
|
||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v3 | ||
|
|
@@ -35,9 +52,122 @@ jobs: | |
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
|
|
||
| - name: Show current locale | ||
| run: locale | ||
|
|
||
| - name: Set UTF-8 enabled locale | ||
| run: | | ||
| sudo locale-gen en_US.UTF-8 | ||
| sudo update-locale LANG=en_US.UTF-8 | ||
| - name: Run pipeline with test data | ||
| uses: Wandalen/[email protected] | ||
| with: | ||
| command: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }} | ||
| attempt_limit: 3 | ||
|
|
||
| motus: | ||
| name: Test mOTUs with workflow parameters | ||
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }} | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| NXF_VER: | ||
| - "21.10.3" | ||
| - "latest-everything" | ||
|
|
||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v2 | ||
|
|
||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v1 | ||
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
|
|
||
| - name: Show current locale | ||
| run: locale | ||
|
|
||
| - name: Set UTF-8 enabled locale | ||
| run: | | ||
| sudo locale-gen en_US.UTF-8 | ||
| sudo update-locale LANG=en_US.UTF-8 | ||
| - name: Prepare the database | ||
| run: | | ||
| wget https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py | ||
| python downloadDB.py > download_db_log.txt | ||
| echo 'tool,db_name,db_params,db_path' > 'database_motus.csv' | ||
| echo 'motus,db_mOTU,,db_mOTU' >> 'database_motus.csv' | ||
| - name: Run pipeline with test data | ||
| uses: Wandalen/[email protected] | ||
| with: | ||
| command: nextflow run ${GITHUB_WORKSPACE} -profile test_motus,docker --outdir ./results --databases ./database_motus.csv | ||
| attempt_limit: 3 | ||
|
|
||
| krakenuniq: | ||
| name: Test KrakenUniq with workflow parameters | ||
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }} | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| NXF_VER: | ||
| - "21.10.3" | ||
| - "latest-everything" | ||
|
|
||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v2 | ||
|
|
||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v1 | ||
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
|
|
||
| - name: Show current locale | ||
| run: locale | ||
|
|
||
| - name: Set UTF-8 enabled locale | ||
| run: | | ||
| sudo locale-gen en_US.UTF-8 | ||
| sudo update-locale LANG=en_US.UTF-8 | ||
| - name: Run pipeline with test data | ||
| # TODO nf-core: You can customise CI pipeline run tests as required | ||
| # For example: adding multiple test runs with different parameters | ||
| # Remember that you can parallelise this by using strategy.matrix | ||
| uses: Wandalen/[email protected] | ||
| with: | ||
| command: nextflow run ${GITHUB_WORKSPACE} -profile test_krakenuniq,docker --outdir ./results | ||
| attempt_limit: 3 | ||
|
|
||
| malt: | ||
| name: Test MALT with workflow parameters | ||
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }} | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| NXF_VER: | ||
| - "21.10.3" | ||
| - "latest-everything" | ||
|
|
||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v2 | ||
|
|
||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v1 | ||
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
|
|
||
| - name: Show current locale | ||
| run: locale | ||
|
|
||
| - name: Set UTF-8 enabled locale | ||
| run: | | ||
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results | ||
| sudo locale-gen en_US.UTF-8 | ||
| sudo update-locale LANG=en_US.UTF-8 | ||
| - name: Run pipeline with test data | ||
| uses: Wandalen/[email protected] | ||
| with: | ||
| command: nextflow run ${GITHUB_WORKSPACE} -profile test_nothing,docker --run_malt --outdir ./results | ||
| attempt_limit: 3 | ||
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|
@@ -10,3 +10,4 @@ testing/ | |
| testing* | ||
| *.pyc | ||
| bin/ | ||
| tests/ | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,6 @@ | ||
| sample,fastq_1,fastq_2 | ||
| SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz | ||
| SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz, | ||
| sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta | ||
| 2611,ERR5766174,ILLUMINA,,,/<path>/<to>/fasta/ERX5474930_ERR5766174_1.fa.gz | ||
| 2612,ERR5766176,ILLUMINA,/<path>/<to>/fastq/ERX5474932_ERR5766176_1.fastq.gz,/<path>/<to>/fastq/ERX5474932_ERR5766176_2.fastq.gz, | ||
| 2612,ERR5766180,ILLUMINA,/<path>/<to>/fastq/ERX5474936_ERR5766180_1.fastq.gz,, | ||
| 2613,ERR5766181,ILLUMINA,/<path>/<to>/fastq/ERX5474937_ERR5766181_1.fastq.gz,/<path>/<to>/fastq/ERX5474937_ERR5766181_2.fastq.gz, | ||
| ERR3201952,ERR3201952,OXFORD_NANOPORE,/<path>/<to>/fastq/ERR3201952.fastq.gz,, |
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