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Fix: read release ID from params, guard against random pick fail when pop. data not avail #50

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Fix: read release ID from params, guard against random pick fail when pop. data not avail #50

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6f7ead2
fix: release ID param
ainefairbrother Dec 1, 2025
3d08e9d
fix: add conditional for the case when no population data is avail
ainefairbrother Dec 4, 2025
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30 changes: 18 additions & 12 deletions nextflow/vcf_prepper/bin/summary_stats.py
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Original file line number Diff line number Diff line change
Expand Up @@ -225,18 +225,24 @@ def main(args=None):

# In case of no representative population - pick a random one
if population_name == "":
population = random.choice(population_data[species_patt])
population_name = population["name"]
freq_info_display = population["name"].replace(
"_", " "
) + population.get("version", "")

file = random.choice(population["files"])
freq_csq_fields.append(
file["short_name"]
+ "_"
+ random.choice(file["include_fields"])["fields"]["af"]
)
# If no population data for this species/assembly (i.e. it's been removed from assets/population_data.json), skip adding population fields
if species_patt not in population_data or not population_data[species_patt]:
population = None
else:
population = random.choice(population_data[species_patt])

if population:
population_name = population["name"]
freq_info_display = population["name"].replace(
"_", " "
) + population.get("version", "")

file = random.choice(population["files"])
freq_csq_fields.append(
file["short_name"]
+ "_"
+ random.choice(file["include_fields"])["fields"]["af"]
)

# add to header and write header to output vcf
if freq_info_display != "":
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2 changes: 1 addition & 1 deletion nextflow/vcf_prepper/modules/local/process_gff.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ process PROCESS_GFF {
shell:
genome = meta.genome
genome_uuid = meta.genome_uuid
release_id = meta.release_id
release_id = params.release_id
version = params.version
out_dir = meta.genome_temp_dir
ini_file = params.ini_file
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