From 5bd80579755b06b74e882b66a1d3b932c3a804ba Mon Sep 17 00:00:00 2001 From: Steffengreiner Date: Thu, 2 Nov 2023 16:03:20 +0100 Subject: [PATCH 1/3] Enable NanoporeParser to check for pod5 and dorado basecaller generated files --- pom.xml | 2 +- .../life/qbic/utils/NanoporeParser.groovy | 40 ++++++++------ .../life/qbic/utils/NanoporeParserSpec.groovy | 22 ++++++++ .../barcode_alignment_.tsv | 0 .../basecalling}/fastq_fail/myfile.fastq.gz | 0 .../basecalling/fastq_fail/myfile2.fastq.gz | 1 + .../basecalling/fastq_fail/myfile3.fastq.gz | 1 + .../basecalling/fastq_fail/myfile4.fastq.gz | 1 + .../basecalling/fastq_fail/myfile5.fastq.gz | 1 + .../basecalling/fastq_pass/myfile1.fastq.gz | 0 .../basecalling/fastq_pass/myfile2.fastq.gz | 0 .../basecalling/fastq_pass/myfile3.fastq.gz | 0 .../basecalling/fastq_pass/myfile4.fastq.gz | 0 .../basecalling/fastq_pass/myfile5.fastq.gz | 0 .../guppy_basecall_client_log-.log | 0 .../basecalling/sequencing_summary_.txt | 0 .../basecalling/sequencing_telemetry_.js | 0 .../fast5_skip/myfile.fast5 | 1 + .../fast5_skip/myfile2.fast5 | 1 + .../fast5_skip/myfile3.fast5 | 1 + .../fast5_skip/myfile4.fast5 | 1 + .../fast5_skip/myfile5.fast5 | 1 + .../final_summary_.txt | 17 ++++++ .../report_.md | 52 +++++++++++++++++++ .../sequencing_summary_.txt | 0 .../unknown_file.new | 0 .../unknown_folder/subfolder_file.here | 0 .../barcode_alignment_.tsv | 0 .../basecalling/fastq_fail/myfile.fastq.gz | 1 + .../basecalling/fastq_fail/myfile2.fastq.gz | 1 + .../basecalling/fastq_fail/myfile3.fastq.gz | 1 + .../basecalling/fastq_fail/myfile4.fastq.gz | 1 + .../basecalling/fastq_fail/myfile5.fastq.gz | 1 + .../basecalling/fastq_pass/myfile1.fastq.gz | 0 .../basecalling/fastq_pass/myfile2.fastq.gz | 0 .../basecalling/fastq_pass/myfile3.fastq.gz | 0 .../basecalling/fastq_pass/myfile4.fastq.gz | 0 .../basecalling/fastq_pass/myfile5.fastq.gz | 0 .../guppy_basecall_client_log-.log | 0 .../basecalling/sequencing_summary_.txt | 0 .../basecalling/sequencing_telemetry_.js | 0 .../fast5_skip/myfile.fast5 | 1 + .../fast5_skip/myfile2.fast5 | 1 + .../fast5_skip/myfile3.fast5 | 1 + .../fast5_skip/myfile4.fast5 | 1 + .../fast5_skip/myfile5.fast5 | 1 + .../final_summary_.txt | 17 ++++++ .../pod5_skip/myfile.pod5 | 1 + .../pod5_skip/myfile2.pod5 | 1 + .../pod5_skip/myfile3.pod5 | 1 + .../pod5_skip/myfile4.pod5 | 1 + .../pod5_skip/myfile5.pod5 | 1 + .../report_.md | 52 +++++++++++++++++++ .../sequencing_summary_.txt | 0 .../unknown_file.new | 0 .../unknown_folder/subfolder_file.here | 0 .../fastq_fail/myfile1.fastq.gz | 0 .../fastq_fail/myfile2.fastq.gz | 1 - .../fastq_fail/myfile3.fastq.gz | 1 - .../fastq_fail/myfile4.fastq.gz | 1 - .../fastq_fail/myfile5.fastq.gz | 1 - 61 files changed, 208 insertions(+), 22 deletions(-) create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/barcode_alignment_.tsv rename src/test/resources/dummyFileSystem/nanopore-instrument-output/{validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a => fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling}/fastq_fail/myfile.fastq.gz (100%) create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile2.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile3.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile4.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile5.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile1.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile2.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile3.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile4.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile5.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/guppy_basecall_client_log-.log create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/sequencing_summary_.txt create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/sequencing_telemetry_.js create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile.fast5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile2.fast5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile3.fast5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile4.fast5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile5.fast5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/sequencing_summary_.txt create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_file.new create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_folder/subfolder_file.here create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/barcode_alignment_.tsv create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile2.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile3.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile4.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile5.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile1.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile2.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile3.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile4.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile5.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/guppy_basecall_client_log-.log create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/sequencing_summary_.txt create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/sequencing_telemetry_.js create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile.fast5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile2.fast5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile3.fast5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile4.fast5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile5.fast5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile.pod5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile2.pod5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile3.pod5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile4.pod5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile5.pod5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/sequencing_summary_.txt create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_file.new create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_folder/subfolder_file.here create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile1.fastq.gz diff --git a/pom.xml b/pom.xml index fe8e746e..243e5a6b 100644 --- a/pom.xml +++ b/pom.xml @@ -128,7 +128,7 @@ data-model-lib life.qbic - 2.25.0 + 2.27.0 org.mockito diff --git a/src/main/groovy/life/qbic/utils/NanoporeParser.groovy b/src/main/groovy/life/qbic/utils/NanoporeParser.groovy index c1318a1d..e778c2db 100644 --- a/src/main/groovy/life/qbic/utils/NanoporeParser.groovy +++ b/src/main/groovy/life/qbic/utils/NanoporeParser.groovy @@ -3,6 +3,7 @@ package life.qbic.utils import com.fasterxml.jackson.databind.ObjectMapper import groovy.json.JsonSlurper import groovy.util.logging.Log4j2 +import life.qbic.datamodel.instruments.OxfordNanoporeInstrumentOutputDoradoMinimal import life.qbic.datamodel.instruments.OxfordNanoporeInstrumentOutputMinimal import net.jimblackler.jsonschemafriend.Schema import net.jimblackler.jsonschemafriend.SchemaStore @@ -14,7 +15,6 @@ import java.nio.file.Path import java.nio.file.Paths import java.text.ParseException import life.qbic.datamodel.datasets.OxfordNanoporeExperiment - import java.util.stream.Collectors @Log4j2 @@ -95,8 +95,8 @@ class NanoporeParser { jsonStarted = true } if (jsonStarted) { - def split = line.replaceAll("\\s+","").split(":") - if(split.size() == 2 && split[1].replaceAll('"',"").size() <= 1){ + def split = line.replaceAll("\\s+", "").split(":") + if (split.size() == 2 && split[1].replaceAll('"', "").size() <= 1) { log.info("Metadata value ${split[0]} missing in ${reportFile["path"]}") } buffer.append(line) @@ -110,12 +110,11 @@ class NanoporeParser { new File(Paths.get(root.toString(), summaryFile["path"].toString()) as String) .readLines().each { line -> def split = line.split("=") - if(split.size() > 1){ + if (split.size() > 1) { finalMetaData[split[0]] = split[1] - } - else { + } else { log.info("Metadata value ${split[0]} missing in ${summaryFile["path"]}, defaulting to empty value") - finalMetaData[split[0]] = "" + finalMetaData[split[0]] = "" } } return finalMetaData @@ -178,18 +177,25 @@ class NanoporeParser { * @throws net.jimblackler.jsonschemafriend.ValidationException */ private static void validateJson(String json) throws ValidationException { - // Step 1: load schema + // Step 1: load json ObjectMapper objectMapper = new ObjectMapper() Object jsonObject = objectMapper.readValue(json, Object) + SchemaStore schemaStore = new SchemaStore() - Schema schema = schemaStore.loadSchema(OxfordNanoporeInstrumentOutputMinimal.getSchemaAsStream()) Validator validator = new Validator() - validator.validate(schema, jsonObject) + try { + Schema schema = schemaStore.loadSchema(OxfordNanoporeInstrumentOutputMinimal.getSchemaAsStream()) + validator.validate(schema, jsonObject) + } catch (ValidationException ignored) { + Schema schema = schemaStore.loadSchema(OxfordNanoporeInstrumentOutputDoradoMinimal.getSchemaAsStream()) + validator.validate(schema, jsonObject) + } } /* * Converts a file tree into a json object. */ + private static class DirectoryConverter { private static final PREDEFINED_EXTENSIONS = ["fastq.gz"] private static final IGNORED_FOLDERNAMES = ["qc"] @@ -239,11 +245,11 @@ class NanoporeParser { List children = currentDirectory.listFiles() List visibleChildren = children.stream() - .filter(file -> !file.isHidden()).collect(Collectors.toList()); + .filter(file -> !file.isHidden()).collect(Collectors.toList()) for (File file : children) { if (!visibleChildren.contains(file)) { - hiddenFiles.add(file); + hiddenFiles.add(file) } } @@ -252,11 +258,11 @@ class NanoporeParser { return !IGNORED_FOLDERNAMES.contains(currentFolderName) }.collect { file -> - if (file.isFile()) { - convertFile(file.toPath()) - } else if (file.isDirectory()) { - convertDirectory(file.toPath()) - } + if (file.isFile()) { + convertFile(file.toPath()) + } else if (file.isDirectory()) { + convertDirectory(file.toPath()) + } } def convertedDirectory = [ diff --git a/src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy b/src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy index e76af9a1..b4e783e8 100644 --- a/src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy +++ b/src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy @@ -125,6 +125,28 @@ class NanoporeParserSpec extends Specification { thrown(ValidationException) } + def "parsing a valid minimal file structure for dorado based basecalling containing additional unknown files and folder still returns an OxfordNanoporeExperiment Object"() { + given: + def pathToDirectory = Paths.get(exampleDirectoriesRoot, "validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal") + when: + def experiment = NanoporeParser.parseFileStructure(pathToDirectory) + then: + assert experiment instanceof OxfordNanoporeExperiment + // Check that the metadata from the report file has been retrieved + assert experiment.getMeasurements().get(0).getMachineHost() == "PCT0094" + // Check that the metadata from the summary file has been retrieved + assert experiment.getMeasurements().get(0).getLibraryPreparationKit() == "SQK-LSK109-XL" + } + + def "parsing an invalid minimal file structure for dorado based basecalling leads to a ValidationException"() { + given: + def pathToDirectory = Paths.get(exampleDirectoriesRoot, "fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder") + when: + def experiment = NanoporeParser.parseFileStructure(pathToDirectory) + then: + thrown(ValidationException) + } + def "parsing the alternative valid file structure with metadata missing returns an OxfordNanoporeExperiment Object"() { given: def pathToDirectory = Paths.get(exampleDirectoriesRoot, "validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new_minimal") diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/barcode_alignment_.tsv b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/barcode_alignment_.tsv new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile.fastq.gz similarity index 100% rename from src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile.fastq.gz rename to src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile.fastq.gz diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile2.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile2.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile2.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile3.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile3.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile3.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile4.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile4.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile4.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile5.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile5.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile5.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile1.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile1.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile2.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile2.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile3.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile3.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile4.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile4.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile5.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile5.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/guppy_basecall_client_log-.log b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/guppy_basecall_client_log-.log new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/sequencing_summary_.txt b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/sequencing_summary_.txt new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/sequencing_telemetry_.js b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/sequencing_telemetry_.js new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile2.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile2.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile2.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile3.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile3.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile3.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile4.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile4.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile4.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile5.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile5.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile5.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt new file mode 100644 index 00000000..900f4d7e --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt @@ -0,0 +1,17 @@ +instrument=PCT0094 +position=1-A3-D3 +flow_cell_id=PAE24142 +sample_id=QNANO027AE_E19D023a01_200211 +protocol_group_id=20200211_QNANO +protocol=sequencing/sequencing_PRO002_DNA:FLO-PRO002:SQK-LSK109-XL +protocol_run_id=5a7cfc2a-81b0-412d-baa0-51b939cd8e76 +acquisition_run_id=c6028297dff19d01e7c5fba6487de807d1e99c05 +started=2020-02-11T15:52:10.465982+01:00 +acquisition_stopped=2020-02-14T08:39:54.688916+01:00 +processing_stopped=2020-02-14T08:39:58.804639+01:00 +basecalling_enabled=1 +sequencing_summary_file=sequencing_summary_PAE24142_c6028297.txt +fast5_files_in_final_dest=2189 +fast5_files_in_fallback=0 +fastq_files_in_final_dest=2189 +fastq_files_in_fallback=0 diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md new file mode 100644 index 00000000..586d5325 --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md @@ -0,0 +1,52 @@ +Tracking ID +=========== + +{ + "asic_id": "0004A30B0022C63E", + "asic_id_eeprom": "0004A30B0022C63E", + "asic_temp": "32.631687", + "asic_version": "Unknown", + "auto_update": "0", + "auto_update_source": "https://mirror.oxfordnanoportal.com/software/MinKNOW/", + "bream_is_standard": "0", + "configuration_version": "1.0.7", + "device_id": "1-E9-H9", + "device_type": "promethion", + "distribution_status": "stable", + "distribution_version": "19.12.5", + "exp_script_name": "N/A", + "exp_script_purpose": "sequencing_run", + "exp_start_time": "2020-01-28T15:17:38Z", + "flow_cell_id": "PAE26989", + "flow_cell_product_code": "FLO-PRO002", + "guppy_version": "3.2.8+bd67289", + "heatsink_temp": "36.179111", + "hostname": "PCT0094", + "hublett_board_id": "0132136faade2e15", + "hublett_firmware_version": "2.0.12", + "installation_type": "nc", + "ip_address": "", + "local_firmware_file": "1", + "mac_address": "", + "operating_system": "ubuntu 16.04", + "protocol_group_id": "20200128_QNANO", + "protocol_run_id": "", + "protocols_version": "4.3.16", + "run_id": "db9e9383d44d80bbe1e2600c7a7419056610d46d", + "sample_id": "QNANO036AD_E19D023b04", + "satellite_board_id": "0000000000000000", + "satellite_firmware_version": "2.0.12", + "usb_config": "firm_1.2.3_ware#rbt_4.5.6_rbt#ctrl#USB3", + "version": "3.6.1" +} + +Duty Time +========= + +ID: db9e9383d44d80bbe1e2600c7a7419056610d46d + +Channel State,Experiment Time (minutes),State Time (samples), +strand,0,144832342 +strand,1,158421270 +strand,2,378095352 +strand,3,472685319 diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/sequencing_summary_.txt b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/sequencing_summary_.txt new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_file.new b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_file.new new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_folder/subfolder_file.here b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_folder/subfolder_file.here new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/barcode_alignment_.tsv b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/barcode_alignment_.tsv new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile2.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile2.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile2.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile3.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile3.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile3.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile4.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile4.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile4.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile5.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile5.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile5.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile1.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile1.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile2.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile2.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile3.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile3.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile4.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile4.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile5.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile5.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/guppy_basecall_client_log-.log b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/guppy_basecall_client_log-.log new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/sequencing_summary_.txt b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/sequencing_summary_.txt new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/sequencing_telemetry_.js b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/sequencing_telemetry_.js new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile2.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile2.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile2.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile3.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile3.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile3.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile4.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile4.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile4.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile5.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile5.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile5.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt new file mode 100644 index 00000000..900f4d7e --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt @@ -0,0 +1,17 @@ +instrument=PCT0094 +position=1-A3-D3 +flow_cell_id=PAE24142 +sample_id=QNANO027AE_E19D023a01_200211 +protocol_group_id=20200211_QNANO +protocol=sequencing/sequencing_PRO002_DNA:FLO-PRO002:SQK-LSK109-XL +protocol_run_id=5a7cfc2a-81b0-412d-baa0-51b939cd8e76 +acquisition_run_id=c6028297dff19d01e7c5fba6487de807d1e99c05 +started=2020-02-11T15:52:10.465982+01:00 +acquisition_stopped=2020-02-14T08:39:54.688916+01:00 +processing_stopped=2020-02-14T08:39:58.804639+01:00 +basecalling_enabled=1 +sequencing_summary_file=sequencing_summary_PAE24142_c6028297.txt +fast5_files_in_final_dest=2189 +fast5_files_in_fallback=0 +fastq_files_in_final_dest=2189 +fastq_files_in_fallback=0 diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile.pod5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile.pod5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile.pod5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile2.pod5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile2.pod5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile2.pod5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile3.pod5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile3.pod5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile3.pod5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile4.pod5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile4.pod5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile4.pod5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile5.pod5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile5.pod5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile5.pod5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md new file mode 100644 index 00000000..586d5325 --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md @@ -0,0 +1,52 @@ +Tracking ID +=========== + +{ + "asic_id": "0004A30B0022C63E", + "asic_id_eeprom": "0004A30B0022C63E", + "asic_temp": "32.631687", + "asic_version": "Unknown", + "auto_update": "0", + "auto_update_source": "https://mirror.oxfordnanoportal.com/software/MinKNOW/", + "bream_is_standard": "0", + "configuration_version": "1.0.7", + "device_id": "1-E9-H9", + "device_type": "promethion", + "distribution_status": "stable", + "distribution_version": "19.12.5", + "exp_script_name": "N/A", + "exp_script_purpose": "sequencing_run", + "exp_start_time": "2020-01-28T15:17:38Z", + "flow_cell_id": "PAE26989", + "flow_cell_product_code": "FLO-PRO002", + "guppy_version": "3.2.8+bd67289", + "heatsink_temp": "36.179111", + "hostname": "PCT0094", + "hublett_board_id": "0132136faade2e15", + "hublett_firmware_version": "2.0.12", + "installation_type": "nc", + "ip_address": "", + "local_firmware_file": "1", + "mac_address": "", + "operating_system": "ubuntu 16.04", + "protocol_group_id": "20200128_QNANO", + "protocol_run_id": "", + "protocols_version": "4.3.16", + "run_id": "db9e9383d44d80bbe1e2600c7a7419056610d46d", + "sample_id": "QNANO036AD_E19D023b04", + "satellite_board_id": "0000000000000000", + "satellite_firmware_version": "2.0.12", + "usb_config": "firm_1.2.3_ware#rbt_4.5.6_rbt#ctrl#USB3", + "version": "3.6.1" +} + +Duty Time +========= + +ID: db9e9383d44d80bbe1e2600c7a7419056610d46d + +Channel State,Experiment Time (minutes),State Time (samples), +strand,0,144832342 +strand,1,158421270 +strand,2,378095352 +strand,3,472685319 diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/sequencing_summary_.txt b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/sequencing_summary_.txt new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_file.new b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_file.new new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_folder/subfolder_file.here b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_folder/subfolder_file.here new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile1.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile1.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz index a46c98ae..e69de29b 100644 --- a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz @@ -1 +0,0 @@ -This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz index a46c98ae..e69de29b 100644 --- a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz @@ -1 +0,0 @@ -This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz index a46c98ae..e69de29b 100644 --- a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz @@ -1 +0,0 @@ -This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz index a46c98ae..e69de29b 100644 --- a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz @@ -1 +0,0 @@ -This is some text From 24d9a3704babeec7587a6d549fc4adb4ed6bd925 Mon Sep 17 00:00:00 2001 From: Steffengreiner Date: Fri, 3 Nov 2023 13:20:47 +0100 Subject: [PATCH 2/3] Add Full data structure example --- .../life/qbic/utils/NanoporeParserSpec.groovy | 13 +++++ .../barcode_alignment_.tsv | 0 .../basecalling/fastq_fail/myfile.fastq.gz | 1 + .../basecalling/fastq_fail/myfile2.fastq.gz | 1 + .../basecalling/fastq_fail/myfile3.fastq.gz | 1 + .../basecalling/fastq_fail/myfile4.fastq.gz | 1 + .../basecalling/fastq_fail/myfile5.fastq.gz | 1 + .../basecalling/fastq_pass/myfile1.fastq.gz | 0 .../basecalling/fastq_pass/myfile2.fastq.gz | 0 .../basecalling/fastq_pass/myfile3.fastq.gz | 0 .../basecalling/fastq_pass/myfile4.fastq.gz | 0 .../basecalling/fastq_pass/myfile5.fastq.gz | 0 .../guppy_basecall_client_log-.log | 0 .../basecalling/sequencing_summary_.txt | 0 .../basecalling/sequencing_telemetry_.js | 0 .../fast5_skip/myfile.fast5 | 1 + .../fast5_skip/myfile2.fast5 | 1 + .../fast5_skip/myfile3.fast5 | 1 + .../fast5_skip/myfile4.fast5 | 1 + .../fast5_skip/myfile5.fast5 | 1 + .../fastq_fail/myfile1.fastq.gz | 0 .../fastq_fail/myfile2.fastq.gz | 0 .../fastq_fail/myfile3.fastq.gz | 0 .../fastq_fail/myfile4.fastq.gz | 0 .../fastq_fail/myfile5.fastq.gz | 0 .../fastq_pass/myfile1.fastq.gz | 0 .../fastq_pass/myfile2.fastq.gz | 0 .../fastq_pass/myfile3.fastq.gz | 0 .../fastq_pass/myfile4.fastq.gz | 0 .../fastq_pass/myfile5.fastq.gz | 0 .../final_summary_.txt | 17 ++++++ .../pod5_fail/myfile.pod5 | 1 + .../pod5_fail/myfile2.pod5 | 1 + .../pod5_fail/myfile3.pod5 | 1 + .../pod5_fail/myfile4.pod5 | 1 + .../pod5_fail/myfile5.pod5 | 1 + .../pod5_pass/myfile.pod5 | 1 + .../pod5_pass/myfile2.pod5 | 1 + .../pod5_pass/myfile3.pod5 | 1 + .../pod5_pass/myfile4.pod5 | 1 + .../pod5_pass/myfile5.pod5 | 1 + .../pod5_skip/myfile.pod5 | 1 + .../pod5_skip/myfile2.pod5 | 1 + .../pod5_skip/myfile3.pod5 | 1 + .../pod5_skip/myfile4.pod5 | 1 + .../pod5_skip/myfile5.pod5 | 1 + .../report_.md | 52 +++++++++++++++++++ .../sequencing_summary_.txt | 0 .../unknown_file.new | 0 .../unknown_folder/subfolder_file.here | 0 50 files changed, 107 insertions(+) create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/barcode_alignment_.tsv create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile2.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile3.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile4.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile5.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile1.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile2.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile3.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile4.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile5.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/guppy_basecall_client_log-.log create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/sequencing_summary_.txt create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/sequencing_telemetry_.js create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile.fast5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile2.fast5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile3.fast5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile4.fast5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile5.fast5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile1.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile1.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile2.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile3.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile4.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile5.fastq.gz create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile.pod5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile2.pod5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile3.pod5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile4.pod5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile5.pod5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile.pod5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile2.pod5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile3.pod5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile4.pod5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile5.pod5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile.pod5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile2.pod5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile3.pod5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile4.pod5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile5.pod5 create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/sequencing_summary_.txt create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_file.new create mode 100644 src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_folder/subfolder_file.here diff --git a/src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy b/src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy index b4e783e8..5f161a12 100644 --- a/src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy +++ b/src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy @@ -138,6 +138,19 @@ class NanoporeParserSpec extends Specification { assert experiment.getMeasurements().get(0).getLibraryPreparationKit() == "SQK-LSK109-XL" } + def "parsing a valid file structure for dorado based basecalling containing additional unknown files and folder still returns an OxfordNanoporeExperiment Object"() { + given: + def pathToDirectory = Paths.get(exampleDirectoriesRoot, "validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example") + when: + def experiment = NanoporeParser.parseFileStructure(pathToDirectory) + then: + assert experiment instanceof OxfordNanoporeExperiment + // Check that the metadata from the report file has been retrieved + assert experiment.getMeasurements().get(0).getMachineHost() == "PCT0094" + // Check that the metadata from the summary file has been retrieved + assert experiment.getMeasurements().get(0).getLibraryPreparationKit() == "SQK-LSK109-XL" + } + def "parsing an invalid minimal file structure for dorado based basecalling leads to a ValidationException"() { given: def pathToDirectory = Paths.get(exampleDirectoriesRoot, "fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder") diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/barcode_alignment_.tsv b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/barcode_alignment_.tsv new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile2.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile2.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile2.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile3.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile3.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile3.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile4.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile4.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile4.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile5.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile5.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile5.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile1.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile1.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile2.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile2.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile3.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile3.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile4.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile4.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile5.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile5.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/guppy_basecall_client_log-.log b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/guppy_basecall_client_log-.log new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/sequencing_summary_.txt b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/sequencing_summary_.txt new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/sequencing_telemetry_.js b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/sequencing_telemetry_.js new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile2.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile2.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile2.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile3.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile3.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile3.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile4.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile4.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile4.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile5.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile5.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile5.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile1.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile1.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile1.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile1.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile2.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile2.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile3.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile3.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile4.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile4.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile5.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile5.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt new file mode 100644 index 00000000..900f4d7e --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt @@ -0,0 +1,17 @@ +instrument=PCT0094 +position=1-A3-D3 +flow_cell_id=PAE24142 +sample_id=QNANO027AE_E19D023a01_200211 +protocol_group_id=20200211_QNANO +protocol=sequencing/sequencing_PRO002_DNA:FLO-PRO002:SQK-LSK109-XL +protocol_run_id=5a7cfc2a-81b0-412d-baa0-51b939cd8e76 +acquisition_run_id=c6028297dff19d01e7c5fba6487de807d1e99c05 +started=2020-02-11T15:52:10.465982+01:00 +acquisition_stopped=2020-02-14T08:39:54.688916+01:00 +processing_stopped=2020-02-14T08:39:58.804639+01:00 +basecalling_enabled=1 +sequencing_summary_file=sequencing_summary_PAE24142_c6028297.txt +fast5_files_in_final_dest=2189 +fast5_files_in_fallback=0 +fastq_files_in_final_dest=2189 +fastq_files_in_fallback=0 diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile.pod5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile.pod5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile.pod5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile2.pod5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile2.pod5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile2.pod5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile3.pod5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile3.pod5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile3.pod5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile4.pod5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile4.pod5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile4.pod5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile5.pod5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile5.pod5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile5.pod5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile.pod5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile.pod5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile.pod5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile2.pod5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile2.pod5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile2.pod5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile3.pod5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile3.pod5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile3.pod5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile4.pod5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile4.pod5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile4.pod5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile5.pod5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile5.pod5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile5.pod5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile.pod5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile.pod5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile.pod5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile2.pod5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile2.pod5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile2.pod5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile3.pod5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile3.pod5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile3.pod5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile4.pod5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile4.pod5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile4.pod5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile5.pod5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile5.pod5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile5.pod5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md new file mode 100644 index 00000000..586d5325 --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md @@ -0,0 +1,52 @@ +Tracking ID +=========== + +{ + "asic_id": "0004A30B0022C63E", + "asic_id_eeprom": "0004A30B0022C63E", + "asic_temp": "32.631687", + "asic_version": "Unknown", + "auto_update": "0", + "auto_update_source": "https://mirror.oxfordnanoportal.com/software/MinKNOW/", + "bream_is_standard": "0", + "configuration_version": "1.0.7", + "device_id": "1-E9-H9", + "device_type": "promethion", + "distribution_status": "stable", + "distribution_version": "19.12.5", + "exp_script_name": "N/A", + "exp_script_purpose": "sequencing_run", + "exp_start_time": "2020-01-28T15:17:38Z", + "flow_cell_id": "PAE26989", + "flow_cell_product_code": "FLO-PRO002", + "guppy_version": "3.2.8+bd67289", + "heatsink_temp": "36.179111", + "hostname": "PCT0094", + "hublett_board_id": "0132136faade2e15", + "hublett_firmware_version": "2.0.12", + "installation_type": "nc", + "ip_address": "", + "local_firmware_file": "1", + "mac_address": "", + "operating_system": "ubuntu 16.04", + "protocol_group_id": "20200128_QNANO", + "protocol_run_id": "", + "protocols_version": "4.3.16", + "run_id": "db9e9383d44d80bbe1e2600c7a7419056610d46d", + "sample_id": "QNANO036AD_E19D023b04", + "satellite_board_id": "0000000000000000", + "satellite_firmware_version": "2.0.12", + "usb_config": "firm_1.2.3_ware#rbt_4.5.6_rbt#ctrl#USB3", + "version": "3.6.1" +} + +Duty Time +========= + +ID: db9e9383d44d80bbe1e2600c7a7419056610d46d + +Channel State,Experiment Time (minutes),State Time (samples), +strand,0,144832342 +strand,1,158421270 +strand,2,378095352 +strand,3,472685319 diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/sequencing_summary_.txt b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/sequencing_summary_.txt new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_file.new b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_file.new new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_folder/subfolder_file.here b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_folder/subfolder_file.here new file mode 100644 index 00000000..e69de29b From 8649a58e663831945f78d108c8bba189494ffcd8 Mon Sep 17 00:00:00 2001 From: Steffengreiner Date: Fri, 3 Nov 2023 16:51:47 +0100 Subject: [PATCH 3/3] Add JD --- src/main/groovy/life/qbic/utils/NanoporeParser.groovy | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/main/groovy/life/qbic/utils/NanoporeParser.groovy b/src/main/groovy/life/qbic/utils/NanoporeParser.groovy index e778c2db..8362a035 100644 --- a/src/main/groovy/life/qbic/utils/NanoporeParser.groovy +++ b/src/main/groovy/life/qbic/utils/NanoporeParser.groovy @@ -184,9 +184,11 @@ class NanoporeParser { SchemaStore schemaStore = new SchemaStore() Validator validator = new Validator() try { + //Validate against Fast5 Based Oxford Measurement Schema schema = schemaStore.loadSchema(OxfordNanoporeInstrumentOutputMinimal.getSchemaAsStream()) validator.validate(schema, jsonObject) } catch (ValidationException ignored) { + //Validate against Pod5 Based Oxford Measurement Schema schema = schemaStore.loadSchema(OxfordNanoporeInstrumentOutputDoradoMinimal.getSchemaAsStream()) validator.validate(schema, jsonObject) }