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"])