test

Test Datasets

In this folder, there are test datasets for VirusWarn-Flu which were downloaded from OpenFlu.

The corresponding metadata files couldn't be downloaded due to an error, so alternative metadata files with only Isolate Name and Collection Date were prepared.

Influenza A H1N1

With the following commands and data set, the mode subtype can be tested for Influenza A H1N1pdm.

Running test set

nextflow run main.nf \
     -profile conda,local \
     --fasta 'test/openflu_h1n1.fasta'

Running test set with metadata

nextflow run main.nf \
     -profile conda,local \
     --fasta 'test/openflu_h1n1.fasta' \
     --metadata 'test/metadata_h1n1.xlsx'

Dataset

The dataset includes 56 sequences and can be downloaded with the following filters:

Filter	Value
Virus type	A
H subtype	1
N subtype	1
Country	Germany
Collection Date From	2019-01-01
Collection Date To	2019-12-31

Influenza A H3N2

With the following commands and data set, the mode subtype can be tested for Influenza A H3N2.

Running test set

nextflow run main.nf \
     -profile conda,local \
     --fasta 'test/openflu_h3n2.fasta' \
     --subtype 'h3n2'

Running test set with metadata

nextflow run main.nf \
     -profile conda,local \
     --fasta 'test/openflu_h3n2.fasta' \
     --metadata 'test/metadata_h3n2.xlsx' \
     --subtype 'h3n2'

Dataset

The dataset includes 79 sequences and can be downloaded with the following filters:

Filter	Value
Virus type	A
H subtype	3
N subtype	2
Country	Germany
Collection Date From	2019-01-01
Collection Date To	2019-12-31

Influenza B Victoria

With the following commands and data set, the mode subtype can be tested for Influenza B Victoria.

Running test set

nextflow run main.nf \
     -profile conda,local \
     --fasta 'test/openflu_vic.fasta' \
     --subtype 'vic'

Running test set with metadata

nextflow run main.nf \
     -profile conda,local \
     --fasta 'test/openflu_vic.fasta' \
     --metadata 'test/metadata_vic.xlsx' \
     --subtype 'vic'

Dataset

The dataset includes 2 sequences and can be downloaded with the following filters:

Filter	Value
Virus type	B
Lineage	Victoria
Country	Germany
Collection Date From	2019-01-01
Collection Date To	2019-12-31

Combi Set

With the following commands and data set, the mode split can be tested for OpenFlu.

Running test set

nextflow run main.nf \
     -profile conda,local \
     --fasta 'test/openflu_combi.fasta' \
     --split 'OpenFlu'

Running test set with metadata

nextflow run main.nf \
     -profile conda,local \
     --fasta 'test/openflu_combi.fasta' \
     --metadata 'test/metadata_combi.xlsx' \
     --split 'OpenFlu'

Dataset

The combi dataset includes all sequences from the three datasets above.