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latest updates based on testing (#137)
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* latest updates based on testing

* updated test parameters
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@charles-cowart
charles-cowart committed Mar 27, 2024
1 parent baf690a commit 04d7af0
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Showing 2 changed files with 19 additions and 15 deletions.
12 changes: 8 additions & 4 deletions sequence_processing_pipeline/NuQCJob.py
View file
Expand Up @@ -83,7 +83,8 @@ def __init__(self, fastq_root_dir, output_path, sample_sheet_path,
self.queue_name = queue_name
self.node_count = node_count
self.wall_time_limit = wall_time_limit
self.jmem = jmem
# raise an Error if jmem is not a valid floating point value.
self.jmem = float(jmem)
self.fastp_path = fastp_path
self.minimap2_path = minimap2_path
self.samtools_path = samtools_path
Expand Down Expand Up @@ -408,15 +409,18 @@ def _generate_job_script(self, max_bucket_size):
else:
gres_value = 2

# As slurm expects memory sizes to be integer values, convert results
# to int to drop floating point component before passing to jinja2 as
# a string.
if max_bucket_size < gigabyte:
mod_wall_time_limit = self.wall_time_limit
mod_jmem = self.jmem
mod_jmem = str(int(self.jmem))
elif max_bucket_size < (2 * gigabyte):
mod_wall_time_limit = self.wall_time_limit * 1.5
mod_jmem = self.jmem * 4.5
mod_jmem = str(int(self.jmem * 4.5))
else:
mod_wall_time_limit = self.wall_time_limit * 2
mod_jmem = self.jmem * 7.5
mod_jmem = str(int(self.jmem * 7.5))

job_script_path = join(self.output_path, 'process_all_fastq_files.sh')
template = self.jinja_env.get_template("nuqc_job.sh")
Expand Down
22 changes: 11 additions & 11 deletions sequence_processing_pipeline/tests/test_NuQCJob.py
View file
Expand Up @@ -591,7 +591,7 @@ def test_nuqcjob_creation(self):
with self.assertRaises(PipelineError) as e:
NuQCJob(self.fastq_root_path, self.output_path,
'not/path/to/sample/sheet', self.mmi_db_paths,
'queue_name', 1, 1440, '8gb',
'queue_name', 1, 1440, '8',
'fastp', 'minimap2', 'samtools', [], self.qiita_job_id,
1000, '')

Expand All @@ -606,7 +606,7 @@ def test_nuqcjob_creation(self):

nuqcjob = NuQCJob(self.fastq_root_path, self.output_path,
self.tmp_file_path, self.mmi_db_paths,
'queue_name', 1, 1440, '8gb',
'queue_name', 1, 1440, '8',
'fastp', 'minimap2', 'samtools', [],
self.qiita_job_id, 1000, '')

Expand All @@ -624,22 +624,22 @@ def test_nuqcjob_creation(self):
"sample-sheet."):
NuQCJob(self.fastq_root_path, self.output_path,
self.tmp_file_path, self.mmi_db_paths,
'queue_name', 1, 1440, '8gb',
'queue_name', 1, 1440, '8',
'fastp', 'minimap2', 'samtools', [], self.qiita_job_id,
1000, '')

with self.assertRaisesRegex(ValueError, "'FALSE' is not a valid value"
" for HumanFiltering"):
NuQCJob(self.fastq_root_path, self.output_path,
self.bad_sheet_bools_path, self.mmi_db_paths,
'queue_name', 1, 1440, '8gb',
'queue_name', 1, 1440, '8',
'fastp', 'minimap2', 'samtools', [], self.qiita_job_id,
1000, '')

def test_error_msg_from_logs(self):
job = NuQCJob(self.fastq_root_path, self.output_path,
self.good_sample_sheet_path, self.mmi_db_paths,
'queue_name', 1, 1440, '8gb',
'queue_name', 1, 1440, '8',
'fastp', 'minimap2', 'samtools', [],
self.qiita_job_id, 1000, '')

Expand Down Expand Up @@ -668,14 +668,14 @@ def test_assay_value(self):
" valid sample-sheet."):
NuQCJob(self.fastq_root_path, self.output_path,
self.bad_sample_sheet_path, self.mmi_db_paths,
'queue_name', 1, 1440, '8gb',
'queue_name', 1, 1440, '8',
'fastp', 'minimap2', 'samtools', [], self.qiita_job_id,
1000, '')

def test_audit(self):
job = NuQCJob(self.fastq_root_path, self.output_path,
self.good_sample_sheet_path, self.mmi_db_paths,
'queue_name', 1, 1440, '8gb',
'queue_name', 1, 1440, '8',
'fastp', 'minimap2', 'samtools', [], self.qiita_job_id,
1000, '')

Expand Down Expand Up @@ -1105,7 +1105,7 @@ def test_completed_file_generation(self):

job = NuQCJob(self.fastq_root_path, self.output_path,
self.good_sample_sheet_path, double_db_paths,
'queue_name', 1, 1440, '8gb',
'queue_name', 1, 1440, '8',
'fastp', 'minimap2', 'samtools', [], self.qiita_job_id,
1000, '')

Expand All @@ -1128,7 +1128,7 @@ def test_completed_file_generation_some_failures(self):

job = NuQCJob(self.fastq_root_path, self.output_path,
self.good_sample_sheet_path, double_db_paths,
'queue_name', 1, 1440, '8gb',
'queue_name', 1, 1440, '8',
'fastp', 'minimap2', 'samtools', [], self.qiita_job_id,
1000, '')

Expand All @@ -1140,7 +1140,7 @@ def test_generate_job_script(self):
double_db_paths = ["db_path/mmi_1.db", "db_path/mmi_2.db"]
job = NuQCJob(self.fastq_root_path, self.output_path,
self.good_sample_sheet_path, double_db_paths,
'queue_name', 1, 1440, '8gb',
'queue_name', 1, 1440, '8',
'fastp', 'minimap2', 'samtools', [], self.qiita_job_id,
1000, '')

Expand All @@ -1153,7 +1153,7 @@ def test_regular_expressions(self):
double_db_paths = ["db_path/mmi_1.db", "db_path/mmi_2.db"]
job = NuQCJob(self.fastq_root_path, self.output_path,
self.good_sample_sheet_path, double_db_paths,
'queue_name', 1, 1440, '8gb',
'queue_name', 1, 1440, '8',
'fastp', 'minimap2', 'samtools', [], self.qiita_job_id,
1000, '')

Expand Down

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