diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 4a45b5a2..b74211de 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,10 +1,13 @@ -name: nf-core CI # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors +name: nf-core CI on: push: branches: - - dev + - "dev" pull_request: + branches: + - "dev" + - "master" release: types: [published] workflow_dispatch: @@ -15,16 +18,31 @@ env: NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity concurrency: - group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} cancel-in-progress: true jobs: + define_nxf_versions: + name: Choose nextflow versions to test against depending on target branch + runs-on: ubuntu-latest + outputs: + matrix: ${{ steps.nxf_versions.outputs.matrix }} + steps: + - id: nxf_versions + run: | + if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then + echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT + else + echo matrix='["latest-everything", "23.10.0"]' | tee -a $GITHUB_OUTPUT + fi + test: name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})" # Only run on push if this is the nf-core dev branch (merged PRs) if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/eager') }}" runs-on: ubuntu-latest strategy: + fail-fast: false matrix: NXF_VER: - "24.04.2" diff --git a/.gitignore b/.gitignore index 23b0c7de..aaae2881 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,4 @@ testing* *.pyc null/ .nf-test* + diff --git a/conf/test.config b/conf/test.config index e358134a..18c376e7 100644 --- a/conf/test.config +++ b/conf/test.config @@ -38,6 +38,7 @@ params { run_bamfiltering = true bamfiltering_minreadlength = 30 bamfiltering_mappingquality = 37 + bamfiltering_savefilteredbams = true // Map Stats run_bedtools_coverage = true diff --git a/nf-test.config b/nf-test.config new file mode 100644 index 00000000..43c9704c --- /dev/null +++ b/nf-test.config @@ -0,0 +1,14 @@ +config { + + testsDir "tests" + workDir ".nf-test" + configFile "tests/nextflow.config" + profile "" + + // load the necessary plugins + plugins { + load "nft-bam@0.3.0" + load "nft-utils@0.0.3" + } + +} diff --git a/tests/nextflow.config b/tests/nextflow.config new file mode 100644 index 00000000..c19b1ad0 --- /dev/null +++ b/tests/nextflow.config @@ -0,0 +1,5 @@ +/* +======================================================================================== + Nextflow config file for running tests +======================================================================================== +*/ diff --git a/tests/test.nf.test b/tests/test.nf.test new file mode 100644 index 00000000..45346596 --- /dev/null +++ b/tests/test.nf.test @@ -0,0 +1,95 @@ +nextflow_pipeline { + + name "Test pipeline: NFCORE_EAGER" + script "main.nf" + tag "pipeline" + tag "nfcore_eager" + tag "test" + + test("test_profile") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + + // Each top level results directory should be tested with individual snapshots/variables + // stable_name_ is for files with variable md5sums (i.e. content) so only names will be compared + // stable_content_ is for files with stable md5sums (i.e. content) so md5sums will be compared + // For both cases, use the third argument to specify globs to exclude certain files + // If a directory is fully stable, you can drop `stable_name_*` + // Generate with: nf-test test --tag test --profile docker,test --update-snapshot + // Test with: nf-test test --tag test --profile docker,test + // NOTE: BAMs are always only stable in name, because: + // a) sharding breaks header since the shard that was first is named in the header + // b) the order of the reads in the BAMs is not stable (sorted, but reads that share a start position can be in any order) + // point b) also causes BAIs to be unstable. + + // Check that no files are missing/added + // Command legend: Result directory to index , include dirs?, exclude patterns , exclude pattern list, include patterns + def stable_name_all = getAllFilesFromDir("$outputDir/" , true , ['pipeline_info/*'] , null , ['*', '**/*'] ) + + // Bam filtering + def stable_content_bamfiltering = getAllFilesFromDir("$outputDir/bam_filtering" , true , ['*.{bam,bai}'] , null , ['*.flagstat'] ) + def stable_name_bamfiltering = getAllFilesFromDir("$outputDir/bam_filtering" , true , ['*.flagstat'] , null , ['*.{bam,bai}'] ) + + // Bam input stats + def stable_content_baminputstats = getAllFilesFromDir("$outputDir/bam_input_stats" , true , null , null , ['*.flagstat'] ) + + // Damage estimation + def stable_content_damageestimation = getAllFilesFromDir("$outputDir/damage_estimation" , true , ['**/*.{svg,pdf,log}'] , null , ['**/*.{txt,json}'] ) + def stable_name_damageestimation = getAllFilesFromDir("$outputDir/damage_estimation" , true , ['**/*.{txt,json}'] , null , ['**/*.{svg,pdf,log}'] ) + + // Deduplication + def stable_content_deduplication = getAllFilesFromDir("$outputDir/deduplication" , true , ['*.{bam,bai}'] , null , ['*.flagstat'] ) + def stable_name_deduplication = getAllFilesFromDir("$outputDir/deduplication" , true , ['*.flagstat'] , null , ['*.{bam,bai}'] ) + + // Final_bams + def stable_content_final_bams = getAllFilesFromDir("$outputDir/final_bams" , true , null , null , ['**/*.flagstat'] ) + def stable_name_final_bams = getAllFilesFromDir("$outputDir/final_bams" , true , null , null , ['**/*.{bam,bai}'] ) + + // Mapping + def stable_content_mapping = getAllFilesFromDir("$outputDir/mapping" , true , null , null , ['**/*.flagstat'] ) + def stable_name_mapping = getAllFilesFromDir("$outputDir/mapping" , true , null , null , ['**/*.{bam,bai}'] ) + + // Mapstats + // NOTE: GC content data and plot has minor changes between runs. I suspect this is because of the order of reads that start at the same position being unstable, but I am not sure. + def stable_content_mapstats = getAllFilesFromDir("$outputDir/mapstats" , true , ['**/*.html', '**/mapped_reads_gc-content_distribution.txt', '**/genome_gc_content_per_window.png'], null , ['**/*.{bed,json,txt,log,css,png,js}'] ) + def stable_name_mapstats = getAllFilesFromDir("$outputDir/mapstats" , true , null , null , ['**/*.html', '**/mapped_reads_gc-content_distribution.txt', '**/genome_gc_content_per_window.png'] ) + + // MultiQC + def stable_name_multiqc = getAllFilesFromDir("$outputDir/multiqc" , true , null , null , ['*', '**/*'] ) + + // Preprocessing + def stable_content_preprocessing = getAllFilesFromDir("$outputDir/preprocessing" , true , ['**/*.{zip,log}', '**/*fastp.html'], null , ['**/*'] ) + def stable_name_preprocessing = getAllFilesFromDir("$outputDir/preprocessing" , true , null , null , ['**/*.{zip,log}', '**/*fastp.html'] ) + + assertAll( + { assert workflow.success }, + // This checks that there are no missing or additional output files. + // Also a good starting point to look at all the files in the output folder than need to be checked in subsequent sections. + { assert snapshot( stable_name_all*.name ).match("all_files") }, + + // Checking changes to contents of each section + { assert snapshot( stable_content_bamfiltering , stable_name_bamfiltering*.name ).match("bam_filtering") }, + { assert snapshot( stable_content_baminputstats ).match("bam_input_stats") }, + { assert snapshot( stable_content_damageestimation, stable_name_damageestimation*.name ).match("damage_estimation") }, + { assert snapshot( stable_content_deduplication , stable_name_deduplication*.name ).match("deduplication") }, + { assert snapshot( stable_content_final_bams , stable_name_final_bams*.name ).match("final_bams") }, + // NOTE: The snapshot section for mapping cannot be named 'mapping'. See https://github.com/askimed/nf-test/issues/279 + { assert snapshot( stable_content_mapping , stable_name_mapping*.name ).match("mapping_output") }, + { assert snapshot( stable_content_mapstats , stable_name_mapstats*.name ).match("mapstats") }, + { assert snapshot( stable_name_multiqc*.name ).match("multiqc") }, + { assert snapshot( stable_content_preprocessing , stable_name_preprocessing*.name ).match("preprocessing") }, + + // Versions + { assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() }, + + + ) + } + } +} diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap new file mode 100644 index 00000000..0332e54c --- /dev/null +++ b/tests/test.nf.test.snap @@ -0,0 +1,907 @@ +{ + "all_files": { + "content": [ + [ + "bam_filtering", + "JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_filtered.bam", + "JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_filtered.bam.bai", + 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