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Add extra required conversion settings
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@rernst
rernst committed Feb 15, 2024
1 parent 94848db commit 6ccd9cd
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Showing 2 changed files with 37 additions and 17 deletions.
34 changes: 21 additions & 13 deletions clarity_epp/export/illumina.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ def get_project(projects, urgent=False):
return projects_sorted[0][0] # return project with least amount of samples.


def get_override_cycles(read_len, umi_len, index_len, max_index_len, index_2_orientation):
def get_override_cycles(read_len, umi_len, index_len, max_index_len, index_2_conversion_orientation):
"""Get override cycles per sample."""
read_cycles = ['', '']
index_cycles = ['', '']
Expand All @@ -40,7 +40,7 @@ def get_override_cycles(read_len, umi_len, index_len, max_index_len, index_2_ori
if index_len[idx]:
if index_len[idx] < max_index_len[idx]:
n_bases = max_index_len[idx] - index_len[idx]
if idx == 1 and index_2_orientation == 'F': # Index 2 in forward orientation (NovaSeq X Plus)
if idx == 1 and index_2_conversion_orientation == 'F': # Index 2 in forward orientation (NovaSeq X Plus)
index_cycle = f'N{n_bases}I{index_len[idx]}'
else:
index_cycle = f'I{index_len[idx]}N{n_bases}'
Expand All @@ -60,7 +60,7 @@ def get_override_cycles(read_len, umi_len, index_len, max_index_len, index_2_ori
return override_cycles


def get_samplesheet_samples(sample_artifacts, process, index_2_orientation):
def get_samplesheet_samples(sample_artifacts, process, index_2_conversion_orientation):
families = {}
samplesheet_samples = {}

Expand All @@ -83,12 +83,12 @@ def get_samplesheet_samples(sample_artifacts, process, index_2_orientation):
if sample.udf['Dx Stoftest code'] == config.stoftestcode_wes_duplo:
continue

# Get sample conversion_settings
sample_conversion_setting = config.conversion_settings['default']
# Get sample conversion settings
sample_conversion_setting = config.sample_conversion_settings['default']
newest_protocol = sample.udf['Dx Protocolomschrijving'].split(';')[0]
for protocol_code in config.conversion_settings:
for protocol_code in config.sample_conversion_settings:
if protocol_code in newest_protocol: # Look for protocol code (elid number) in newest protocol
sample_conversion_setting = config.conversion_settings[protocol_code]
sample_conversion_setting = config.sample_conversion_settings[protocol_code]
break

# Get sample override cycles
Expand All @@ -97,7 +97,7 @@ def get_samplesheet_samples(sample_artifacts, process, index_2_orientation):
umi_len=sample_conversion_setting['umi_len'],
index_len=[len(sample_index[0]), len(sample_index[1])],
max_index_len=[process.udf['Index Read 1'], process.udf['Index Read 2']],
index_2_orientation=index_2_orientation
index_2_conversion_orientation=index_2_conversion_orientation
)

# Set family and create if not exist
Expand Down Expand Up @@ -158,10 +158,10 @@ def get_samplesheet_samples(sample_artifacts, process, index_2_orientation):
else:
sample_override_cycles = get_override_cycles(
read_len=[process.udf['Read 1 Cycles'], process.udf['Read 2 Cycles']],
umi_len=config.conversion_settings['default']['umi_len'],
umi_len=config.sample_conversion_settings['default']['umi_len'],
index_len=[len(sample_index[0]), len(sample_index[1])],
max_index_len=[process.udf['Index Read 1'], process.udf['Index Read 2']],
index_2_orientation=index_2_orientation
index_2_conversion_orientation=index_2_conversion_orientation
)

# Add sample to samplesheet_samples
Expand All @@ -170,7 +170,7 @@ def get_samplesheet_samples(sample_artifacts, process, index_2_orientation):
'index_2': sample_index[1],
'override_cycles': sample_override_cycles,
}
if index_2_orientation == 'RC': # Reverse complement index 2
if index_2_conversion_orientation == 'RC': # Reverse complement index 2
samplesheet_samples[sample_sequence_name]['index_2'] = reverse_complement(
samplesheet_samples[sample_sequence_name]['index_2']
)
Expand Down Expand Up @@ -229,19 +229,25 @@ def get_samplesheet_samples(sample_artifacts, process, index_2_orientation):
def create_samplesheet(lims, process_id, output_file):
"""Create illumina samplesheet v2."""
process = Process(lims, id=process_id)
index_2_orientation = config.index_2_orientation[process.type.name]
sequencer_conversion_settings = config.sequencer_conversion_settings[process.type.name]

# Get samples samples per lane
samplesheet_samples = []
for lane in process.analytes()[0]:
sample_artifacts = get_sample_artifacts_from_pool(lims, process.analytes()[0][0])
samplesheet_samples.append(get_samplesheet_samples(sample_artifacts, process, index_2_orientation))
samplesheet_samples.append(
get_samplesheet_samples(
sample_artifacts, process, sequencer_conversion_settings['index_2_conversion_orientation']
)
)

# Create SampleSheet
sample_sheet = [
# Header
"[Header]",
"FileFormatVersion,2",
f"InstrumentPlatform,{sequencer_conversion_settings['instrument_platform']}",
f"IndexOrientation,{sequencer_conversion_settings['index_orientation']}",
f"RunName,{process.udf['Experiment Name']}",
# Reads
"[Reads]",
Expand All @@ -251,6 +257,8 @@ def create_samplesheet(lims, process_id, output_file):
f"Index2Cycles,{process.udf['Index Read 2']}",
# BCLConvert_Settings
"[BCLConvert_Settings]",
f"SoftwareVersion,{sequencer_conversion_settings['software_version']}",
f"FastqCompressionFormat,{sequencer_conversion_settings['fastq_compression_format']}",
f"AdapterRead1,{process.udf['Adapter']}",
f"AdapterRead2,{process.udf['Adapter Read 2']}",
"FindAdaptersWithIndels,true",
Expand Down
20 changes: 16 additions & 4 deletions config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -91,13 +91,25 @@
]

# BCLConvert conversion settings
index_2_orientation = {
sequencer_conversion_settings = {
# Orientation options: F=forward or RC=reverse complement
# https://knowledge.illumina.com/software/general/software-general-reference_material-list/000001800
'Dx Library pool denatureren en laden (NovaSeq) v1.3': 'RC',
'Dx Library pool denatureren en laden (NovaSeqXPlus) v1.0': 'F',
'Dx Library pool denatureren en laden (NovaSeq) v1.3': {
'index_2_conversion_orientation': 'RC',
'instrument_platform': 'NovaSeq',
'index_orientation': 'Forward',
'software_version': '4.1.7',
'fastq_compression_format': 'GZIP',
},
'Dx Library pool denatureren en laden (NovaSeqXPlus) v1.0': {
'index_2_conversion_orientation': 'F',
'instrument_platform': 'NovaSeqXPlus',
'index_orientation': 'Forward',
'software_version': '4.1.7',
'fastq_compression_format': 'GZIP',
},
}
conversion_settings = {
sample_conversion_settings = {
'default': {
'project': 'unknown',
'split_project': False,
Expand Down

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