def init_testdata(directory): run_init( database="testdata/database", reads1="testdata/reads.1.fastq.gz", directory=str(directory), ) with chdir(directory): modify_configuration([("barcode_length_3prime", "21")])
def test_fastq_input(has_filtered_tab, tmp_path): # Use merged reads from already-run pipeline as input for a new run single_reads = has_filtered_tab / "reads" / "2-merged.fastq.gz" directory = tmp_path / "singleend-fastq" run_init( database="testdata/database", single_reads=str(single_reads), directory=str(directory), ) with chdir(directory): modify_configuration([("barcode_length_3prime", "21")]) run_snakemake(targets=["stats/reads.json"])
def test_fasta_input(has_filtered_tab, tmp_path): fasta_path = tmp_path / "justfasta.fasta" convert_fastq_to_fasta( has_filtered_tab / "reads" / "2-merged.fastq.gz", fasta_path, ) directory = tmp_path / "singleend-fasta" run_init( database="testdata/database", single_reads=str(fasta_path), directory=str(directory), ) with chdir(directory): modify_configuration([("barcode_length_3prime", "21")]) run_snakemake(targets=["stats/reads.json"])