CI
843f4b7e37
Build pipeline: viash-hub.htrnaseq.v0.9-4v78w
Source commit: 1bce00e811
Source message: Bump version to v0.9.1
182 lines
9.0 KiB
Plaintext
182 lines
9.0 KiB
Plaintext
import java.nio.file.Files
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import nextflow.exception.WorkflowScriptErrorException
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def viash_config = java.nio.file.Paths.get("${params.rootDir}/target/nextflow/workflows/runner/_viash.yaml")
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def get_version(inputFile) {
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def yamlSlurper = new groovy.yaml.YamlSlurper()
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def loaded_viash_config = yamlSlurper.parse(file(inputFile))
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def version = (loaded_viash_config.version) ? loaded_viash_config.version : "unknown_version"
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println("HT-RNAseq version to be used: ${version}")
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return version
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}
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// Create temporary directory for the publish_dir if it is not defined
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if (!params.containsKey("publish_dir") && params.containsKey("publishDir")) {
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params.publish_dir = params.publishDir
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}
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if (!params.containsKey("publish_dir")) {
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def tempDir = Files.createTempDirectory("demultiplex_runner_integration_test")
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println "Created temp directory: $tempDir"
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// Register shutdown hook to delete it on JVM exit
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Runtime.runtime.addShutdownHook(new Thread({
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try {
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// Delete directory recursively
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Files.walk(tempDir)
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.sorted(Comparator.reverseOrder())
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.forEach { Files.delete(it) }
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println "Deleted temp directory: $tempDir"
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} catch (Exception e) {
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println "Failed to delete temp directory: $e"
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}
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}))
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params.publish_dir = tempDir
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}
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params.fastq_publish_dir = (file(params.publish_dir) / "fastq").toUriString()
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params.results_publish_dir = (file(params.publish_dir) / "results").toUriString()
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// The module inherits the parameters defined before the include statement,
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// therefore any parameters set afterwards will not be used by the module.
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include { runner } from params.rootDir + "/target/nextflow/workflows/runner/main.nf"
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params.resources_test = params.rootDir + "/resources_test"
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workflow test_wf {
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pipeline_version = get_version(viash_config)
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resources_test = file(params.resources_test)
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// results_publish_dir and results_publish_dir are inherited using params
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// but they must be defined in the state as well because viash will check
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// if all arguments are present in the hashmap
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output_ch = Channel.fromList([
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[
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id: "run_1",
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input: resources_test.resolve("10k/SRR14730301"),
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genomeDir: resources_test.resolve("genomeDir/subset/Homo_sapiens/v0.0.3"),
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barcodesFasta: resources_test.resolve("2-wells-with-ids.fasta"),
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annotation: resources_test.resolve("genomeDir/gencode.v41.annotation.gtf.gz"),
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project_id: "foo",
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experiment_id: "bar",
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fastq_publish_dir: params.fastq_publish_dir,
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results_publish_dir: params.results_publish_dir,
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],
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[
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id: "run_2",
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input: resources_test.resolve("10k/SRR14730301"),
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genomeDir: resources_test.resolve("genomeDir/subset/Homo_sapiens/v0.0.3"),
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barcodesFasta: resources_test.resolve("2-wells-with-ids.fasta"),
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annotation: resources_test.resolve("genomeDir/gencode.v41.annotation.gtf.gz"),
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project_id: "foo",
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experiment_id: "bar",
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fastq_publish_dir: params.fastq_publish_dir,
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results_publish_dir: params.results_publish_dir,
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],
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[
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id: "run_3",
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input:resources_test.resolve("10k/SRR14730302"),
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genomeDir: resources_test.resolve("genomeDir/subset/Homo_sapiens/v0.0.3"),
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barcodesFasta: resources_test.resolve("2-wells-with-ids.fasta"),
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annotation: resources_test.resolve("genomeDir/gencode.v41.annotation.gtf.gz"),
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project_id: "foo",
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experiment_id: "bar",
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fastq_publish_dir: params.fastq_publish_dir,
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results_publish_dir: params.results_publish_dir,
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]
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])
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| map { state -> [state.id, state]}
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| runner.run(
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toState: { id, output, state -> output + [orig_input: state.input] }
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)
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| view { output ->
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assert output.size() == 2 : "outputs should contain two elements; [id, file]"
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"Output: $output"
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}
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tosortedlistch = output_ch
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| toSortedList()
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| map {events ->
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assert events.size() == 1, "Expected one events to be output, found ${events.size()}"
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}
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workflow.onComplete = {
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try {
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// Nexflow only allows exceptions generated using the 'error' function (which throws WorkflowScriptErrorException).
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// So in order for the assert statement to work (or allow other errors to let the tests to fail)
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// We need to wrap these in WorkflowScriptErrorException. See https://github.com/nextflow-io/nextflow/pull/4458/files
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// The error message will show up in .nextflow.log
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def fastq_subdir = file("${params.fastq_publish_dir}")
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assert fastq_subdir.isDirectory()
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def found_fastq_folders = fastq_subdir.listFiles().findAll{it.isDirectory()}.collect{it.name}.toSet()
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def expected_run_folders = ["run_1", "run_2", "run_3"].toSet()
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assert found_fastq_folders == expected_run_folders, "Expected correct run folders to be present. Found: ${found_fastq_folders}"
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unique_dirs = [
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"run1": files("${fastq_subdir.toUriString()}/run_1/*_htrnaseq_${pipeline_version}", type: 'any'),
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"run2": files("${fastq_subdir.toUriString()}/run_2/*_htrnaseq_${pipeline_version}", type: 'any'),
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"run3": files("${fastq_subdir.toUriString()}/run_3/*_htrnaseq_${pipeline_version}", type: 'any'),
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]
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assert unique_dirs.every{it.value.size() == 1}
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unique_dirs = unique_dirs.collectEntries{k, v -> [k, v[0]]}
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assert unique_dirs.every{it.value.isDirectory()}
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assert unique_dirs.collect{_key, _value -> _value.name}.toSet().size() == 1
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def expected_samples = [
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"run1": "VH02001612",
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"run2": "VH02001612",
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"run3": "VH02001614"
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]
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unique_dirs.each{_key, _value ->
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def expected_sample = expected_samples[_key]
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def expected_sample_dir = _value.resolve(expected_sample)
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assert expected_sample_dir.isDirectory(), "Expected ${expected_sample} to be present in ${_value}"
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def expected_fastq_files = [
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"A1_R1_001.fastq", "A1_R2_001.fastq",
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"B1_R1_001.fastq", "B1_R2_001.fastq",
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"unknown_R1_001.fastq", "unknown_R2_001.fastq"]
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def found_files = files("${expected_sample_dir}/*.fastq", type: 'any')
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assert found_files.every{it.isFile()}
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assert found_files.collect{it.name}.toSet() == expected_fastq_files.toSet()
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}
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def results_subdir = file("${params.results_publish_dir}")
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assert fastq_subdir.isDirectory()
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def expected_subdir = file("${results_subdir}/foo/bar/data_processed", type: 'any')
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assert expected_subdir.isDirectory()
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def expected_result_dir = files("${expected_subdir}/*_htrnaseq_${pipeline_version}", type: 'any')
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assert expected_result_dir.size() == 1
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expected_result_dir = expected_result_dir[0]
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assert expected_result_dir.isDirectory()
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def expected_esets = ["VH02001612.rds", "VH02001614.rds"]
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def found_esets = files("${expected_result_dir}/esets/*.rds", type: 'any')
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assert found_esets.size() == 2
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assert found_esets.collect{it.name}.toSet() == expected_esets.toSet()
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expected_table_filenames = ["VH02001612.txt", "VH02001614.txt"]
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def found_pdata = files("${expected_result_dir}/pData/*.txt", type: 'any')
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assert found_pdata.size() == 2
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assert found_pdata.collect{it.name}.toSet() == expected_table_filenames.toSet()
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def found_nr_genes_nr_reads = files("${expected_result_dir}/nrReadsNrGenesPerChrom/*.txt", type: 'any')
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assert found_nr_genes_nr_reads.size() == 2
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assert found_nr_genes_nr_reads.collect{it.name}.toSet() == expected_table_filenames.toSet()
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def found_star_logs = files("${expected_result_dir}/starLogs/*.txt", type: 'any')
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assert found_star_logs.size() == 2
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assert found_star_logs.collect{it.name}.toSet() == expected_table_filenames.toSet()
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def star_output = file("${expected_result_dir}/star_output", type: 'any')
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assert star_output.isDirectory()
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assert files("${star_output}/*", type: 'any').collect{it.name}.toSet() == ["VH02001612", "VH02001614"].toSet()
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assert files("${star_output}/VH02001612/*", type: 'any').collect{it.name}.toSet() == ["ACACCGAATT", "GGCTATTGAT"].toSet()
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assert files("${star_output}/VH02001614/*", type: 'any').collect{it.name}.toSet() == ["ACACCGAATT", "GGCTATTGAT"].toSet()
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assert file("${expected_result_dir}/report.html").isFile()
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assert file("${expected_result_dir}/params.yaml").isFile()
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assert file("${expected_result_dir}/fData.gencode.v41.annotation.gtf.gz.txt").isFile()
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} catch (Exception e) {
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throw new WorkflowScriptErrorException("Integration test failed!", e)
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}
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}
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}
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