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