From 24d9a3704babeec7587a6d549fc4adb4ed6bd925 Mon Sep 17 00:00:00 2001 From: Steffengreiner Date: Fri, 3 Nov 2023 13:20:47 +0100 Subject: [PATCH] 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 + 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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 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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 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