From e090fd8ebced74eee54806741f8c8c9a6e7e1307 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 19 Sep 2024 15:55:28 +0200 Subject: [PATCH 1/2] add test for dada2 using no value for the length parameter --- .../dada2/dada2_paired-wolength-tests.yml | 84 +++++++++++++++++++ 1 file changed, 84 insertions(+) create mode 100644 workflows/amplicon/dada2/dada2_paired-wolength-tests.yml diff --git a/workflows/amplicon/dada2/dada2_paired-wolength-tests.yml b/workflows/amplicon/dada2/dada2_paired-wolength-tests.yml new file mode 100644 index 0000000000..781aa76151 --- /dev/null +++ b/workflows/amplicon/dada2/dada2_paired-wolength-tests.yml @@ -0,0 +1,84 @@ +- doc: Test outline for dada---paired + job: + Paired input data: + class: Collection + collection_type: list:paired + elements: + - class: Collection + type: paired + identifier: F3D0 + elements: + - class: File + identifier: forward + location: https://zenodo.org/record/800651/files/F3D0_R1.fastq + - class: File + identifier: reverse + location: https://zenodo.org/record/800651/files/F3D0_R2.fastq + - class: Collection + type: paired + identifier: F3D5 + elements: + - class: File + identifier: forward + location: https://zenodo.org/record/800651/files/F3D5_R1.fastq + - class: File + identifier: reverse + location: https://zenodo.org/record/800651/files/F3D5_R2.fastq + - class: Collection + type: paired + identifier: F3D145 + elements: + - class: File + identifier: forward + location: https://zenodo.org/record/800651/files/F3D145_R1.fastq + - class: File + identifier: reverse + location: https://zenodo.org/record/800651/files/F3D145_R2.fastq + - class: Collection + type: paired + identifier: F3D150 + elements: + - class: File + identifier: forward + location: https://zenodo.org/record/800651/files/F3D150_R1.fastq + - class: File + identifier: reverse + location: https://zenodo.org/record/800651/files/F3D150_R2.fastq + - class: Collection + type: paired + identifier: Mock + elements: + - class: File + identifier: forward + location: https://zenodo.org/record/800651/files/Mock_R1.fastq + - class: File + identifier: reverse + location: https://zenodo.org/record/800651/files/Mock_R2.fastq + Pool samples: 'FALSE' + Cached reference database: silva_132 + outputs: + Sequence Table: + path: test-data/Sequence Table.dada2_sequencetable + asserts: + - has_n_columns: + n: 6 + - has_n_lines: + n: 171 + Counts: + path: test-data/Counts.tabular + asserts: + - has_n_columns: + n: 8 + - has_n_lines: + n: 6 + Taxonomy: + ftype: tabular + sorted: true + asserts: + - has_text: + text: Firmicutes + n: 131 + - has_n_columns: + n: 7 + - has_n_lines: + n: 171 From b8f0e0a7198af14a4db93cbcecf63bf11b92f4b7 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 19 Sep 2024 16:38:33 +0200 Subject: [PATCH 2/2] add new test as list element --- .../amplicon/dada2/dada2_paired-tests.yml | 84 +++++++++++++++++++ .../dada2/dada2_paired-wolength-tests.yml | 84 ------------------- 2 files changed, 84 insertions(+), 84 deletions(-) delete mode 100644 workflows/amplicon/dada2/dada2_paired-wolength-tests.yml diff --git a/workflows/amplicon/dada2/dada2_paired-tests.yml b/workflows/amplicon/dada2/dada2_paired-tests.yml index 50d9c177d2..2d94b8cb3b 100644 --- a/workflows/amplicon/dada2/dada2_paired-tests.yml +++ b/workflows/amplicon/dada2/dada2_paired-tests.yml @@ -84,3 +84,87 @@ n: 7 - has_n_lines: n: 171 +- doc: Same without specifying trunction length + job: + Paired input data: + class: Collection + collection_type: list:paired + elements: + - class: Collection + type: paired + identifier: F3D0 + elements: + - class: File + identifier: forward + location: https://zenodo.org/record/800651/files/F3D0_R1.fastq + - class: File + identifier: reverse + location: https://zenodo.org/record/800651/files/F3D0_R2.fastq + - class: Collection + type: paired + identifier: F3D5 + elements: + - class: File + identifier: forward + location: https://zenodo.org/record/800651/files/F3D5_R1.fastq + - class: File + identifier: reverse + location: https://zenodo.org/record/800651/files/F3D5_R2.fastq + - class: Collection + type: paired + identifier: F3D145 + elements: + - class: File + identifier: forward + location: https://zenodo.org/record/800651/files/F3D145_R1.fastq + - class: File + identifier: reverse + location: https://zenodo.org/record/800651/files/F3D145_R2.fastq + - class: Collection + type: paired + identifier: F3D150 + elements: + - class: File + identifier: forward + location: https://zenodo.org/record/800651/files/F3D150_R1.fastq + - class: File + identifier: reverse + location: https://zenodo.org/record/800651/files/F3D150_R2.fastq + - class: Collection + type: paired + identifier: Mock + elements: + - class: File + identifier: forward + location: https://zenodo.org/record/800651/files/Mock_R1.fastq + - class: File + identifier: reverse + location: https://zenodo.org/record/800651/files/Mock_R2.fastq + Pool samples: 'FALSE' + Cached reference database: silva_132 + outputs: + Sequence Table: + path: test-data/Sequence Table.dada2_sequencetable + asserts: + - has_n_columns: + n: 6 + - has_n_lines: + n: 171 + Counts: + path: test-data/Counts.tabular + asserts: + - has_n_columns: + n: 8 + - has_n_lines: + n: 6 + Taxonomy: + ftype: tabular + sorted: true + asserts: + - has_text: + text: Firmicutes + n: 131 + - has_n_columns: + n: 7 + - has_n_lines: + n: 171 \ No newline at end of file diff --git a/workflows/amplicon/dada2/dada2_paired-wolength-tests.yml b/workflows/amplicon/dada2/dada2_paired-wolength-tests.yml deleted file mode 100644 index 781aa76151..0000000000 --- a/workflows/amplicon/dada2/dada2_paired-wolength-tests.yml +++ /dev/null @@ -1,84 +0,0 @@ -- doc: Test outline for dada---paired - job: - Paired input data: - class: Collection - collection_type: list:paired - elements: - - class: Collection - type: paired - identifier: F3D0 - elements: - - class: File - identifier: forward - location: https://zenodo.org/record/800651/files/F3D0_R1.fastq - - class: File - identifier: reverse - location: https://zenodo.org/record/800651/files/F3D0_R2.fastq - - class: Collection - type: paired - identifier: F3D5 - elements: - - class: File - identifier: forward - location: https://zenodo.org/record/800651/files/F3D5_R1.fastq - - class: File - identifier: reverse - location: https://zenodo.org/record/800651/files/F3D5_R2.fastq - - class: Collection - type: paired - identifier: F3D145 - elements: - - class: File - identifier: forward - location: https://zenodo.org/record/800651/files/F3D145_R1.fastq - - class: File - identifier: reverse - location: https://zenodo.org/record/800651/files/F3D145_R2.fastq - - class: Collection - type: paired - identifier: F3D150 - elements: - - class: File - identifier: forward - location: https://zenodo.org/record/800651/files/F3D150_R1.fastq - - class: File - identifier: reverse - location: https://zenodo.org/record/800651/files/F3D150_R2.fastq - - class: Collection - type: paired - identifier: Mock - elements: - - class: File - identifier: forward - location: https://zenodo.org/record/800651/files/Mock_R1.fastq - - class: File - identifier: reverse - location: https://zenodo.org/record/800651/files/Mock_R2.fastq - Pool samples: 'FALSE' - Cached reference database: silva_132 - outputs: - Sequence Table: - path: test-data/Sequence Table.dada2_sequencetable - asserts: - - has_n_columns: - n: 6 - - has_n_lines: - n: 171 - Counts: - path: test-data/Counts.tabular - asserts: - - has_n_columns: - n: 8 - - has_n_lines: - n: 6 - Taxonomy: - ftype: tabular - sorted: true - asserts: - - has_text: - text: Firmicutes - n: 131 - - has_n_columns: - n: 7 - - has_n_lines: - n: 171