def test_flash(pipeline_dir):
# Test using FLASH and parsing its log output
with chdir(pipeline_dir):
modify_configuration(settings=[("merge_program", "flash")])
run_snakemake(targets=["stats/reads.json"])
# Ensure FLASH was actually run
assert (pipeline_dir / "reads/2-flash.log").exists()
def filtered_tab_session(tmp_path_factory):
"""Generate iteration-01/filtered.tab.gz"""
pipeline_dir = tmp_path_factory.mktemp("pipedir") / "pipedir"
init_testdata(pipeline_dir)
with chdir(pipeline_dir):
run_snakemake(targets=["iteration-01/filtered.tab.gz"])
return pipeline_dir
def test_primers(pipeline_dir):
# Test whether specifying primer sequences leads to a SyntaxError
with chdir(pipeline_dir):
modify_configuration(settings=[
("forward_primers", "['CGTGA']"),
("reverse_primers", "['TTCAC']"),
], )
run_snakemake(dryrun=True)
def test_snakemake_final(has_filtered_tab):
with chdir(has_filtered_tab):
run_snakemake(targets=["nofinal"])
assert (has_filtered_tab / "iteration-01/new_V_germline.tab").exists()
assert not (has_filtered_tab / "final/assigned.tab.gz").exists()
with chdir(has_filtered_tab):
run_snakemake()
assert (has_filtered_tab / "final/assigned.tab.gz").exists()
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"])
def test_only_forward_primer(pipeline_dir):
# issue #107 (broken symlink)
with chdir(pipeline_dir):
modify_configuration(settings=[("forward_primers", "['CGTGA']")])
# Create some dummy files so we don’t need to run irrelevant steps of the pipeline
r = Path("reads")
r.mkdir()
with xopen(r / "2-merged.fastq.gz", "w") as f:
pass
s = Path("stats")
s.mkdir()
with open(s / "merging-successful", "w") as f:
pass
with open(s / "reads.json", "w") as f:
f.write('{"total": 0}')
with open(s / "trimmed.json", "w") as f:
f.write('{"trimmed": 0}')
run_snakemake(targets=["reads/sequences.fasta.gz"])
def test_snakemake_exact_tab(has_filtered_tab):
with chdir(has_filtered_tab):
run_snakemake(targets=["iteration-01/exact.tab"])
assert (has_filtered_tab / "iteration-01/exact.tab").exists()
def test_dryrun(pipeline_dir):
with chdir(pipeline_dir):
run_snakemake(dryrun=True)