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[WIP] fix dada2 workflows #524

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84 changes: 84 additions & 0 deletions workflows/amplicon/dada2/dada2_paired-tests.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
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