def test_pipes(tmpdir_function, kraken_db, krona_db, input_bam):
runner = snake.SnakemakeRunner(workdir=tmpdir_function)
override_config = {
'kraken_db': kraken_db,
'krona_db': krona_db,
}
runner.set_override_config(override_config)
runner.setup()
runner.link_samples([input_bam], destination='per_sample', link_transform=snake.rename_raw_bam)
runner.create_sample_files(sample_files=['samples_metagenomics'])
kraken_out = join(
runner.config['data_dir'], runner.config['subdirs']['metagenomics'],
'.'.join([os.path.splitext(os.path.basename(input_bam))[0], 'raw', 'kraken.report'])
)
krona_out = join(
runner.config['data_dir'], runner.config['subdirs']['metagenomics'],
'.'.join([os.path.splitext(os.path.basename(input_bam))[0], 'raw', 'kraken.krona.html'])
)
# runner.run(['all_metagenomics'])
runner.run([kraken_out, krona_out])
assert os.path.getsize(os.path.join(runner.workdir, kraken_out)) > 0
assert os.path.getsize(os.path.join(runner.workdir, krona_out)) > 0
def test_pipes(tmpdir, bwa_db, taxonomy_db, input_bam):
runner = snake.SnakemakeRunner(workdir=str(tmpdir))
override_config = {
'align_rna_db': bwa_db,
'taxonomy_db': taxonomy_db,
}
runner.set_override_config(override_config)
runner.setup()
runner.link_samples([input_bam],
destination='per_sample',
link_transform=snake.rename_raw_bam)
runner.create_sample_files(sample_files=['samples_metagenomics'])
report_out = join(
runner.workdir, runner.data_dir,
runner.config['subdirs']['metagenomics'], '.'.join([
os.path.splitext(os.path.basename(input_bam))[0],
'raw.rna_bwa.report'
]))
bam_out = join(
runner.workdir, runner.data_dir,
runner.config['subdirs']['metagenomics'], '.'.join([
os.path.splitext(os.path.basename(input_bam))[0], 'raw.rna_bwa.bam'
]))
runner.run([report_out])
assert os.path.getsize(report_out) > 0
assert os.path.getsize(bam_out) > 0
def test_pipes(tmpdir, diamond_db, taxonomy_db, krona_db, input_bam):
runner = snake.SnakemakeRunner(workdir=str(tmpdir))
override_config = {
'diamond_db': diamond_db,
'taxonomy_db': taxonomy_db,
'krona_db': krona_db,
}
runner.set_override_config(override_config)
runner.setup()
runner.link_samples([input_bam],
destination='per_sample',
link_transform=snake.rename_raw_bam)
runner.create_sample_files(sample_files=['samples_metagenomics'])
krona_out = join(
runner.workdir, runner.data_dir,
runner.config['subdirs']['metagenomics'], '.'.join([
os.path.splitext(os.path.basename(input_bam))[0], 'raw',
'diamond.krona.html'
]))
diamond_out = join(
runner.workdir, runner.data_dir,
runner.config['subdirs']['metagenomics'], '.'.join([
os.path.splitext(os.path.basename(input_bam))[0], 'raw',
'diamond.report'
]))
runner.run([krona_out])
assert os.path.getsize(diamond_out) > 0
assert os.path.getsize(krona_out) > 0