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Merge branch 'dev' into add-rtgtools-bndeval
2 parents 43937ff + b932094 commit cb13c6f

20 files changed

Lines changed: 425 additions & 85 deletions

‎bin/merge_sompy_features.py‎

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#!/usr/bin/env python
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# Copyright 2025 - GHGA
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# Author: Kuebra Narci - @kubranarci
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'''
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Generates a CSV file from a VCF
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Expected usage:
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$ python split_sompy_features.py <vcf_file> <prefix>
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Use --help for more information.
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'''
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import csv
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import argparse
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from collections import defaultdict
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import os
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KEY_COLUMNS = ["CHROM", "POS", "tag"]
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FIELDS_TO_EXTRACT = ["CHROM", "POS", "tag", "REF", "REF.truth", "ALT", "ALT.truth", "QUAL", "FILTER"]
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FIELDS_TO_SUFFIX = ["REF", "ALT"]
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def extract_sample_suffix(filename):
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"""Extract sample suffix from filename (without extension)."""
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return os.path.splitext(os.path.basename(filename))[0]
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def load_csv_by_key(filepath, suffix):
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"""Read a CSV file, filter relevant fields, and suffix REF/ALT."""
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with open(filepath, newline='') as f:
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reader = csv.DictReader(f)
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data = {}
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for row in reader:
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key = tuple(row[k] for k in KEY_COLUMNS)
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filtered = {}
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for field in FIELDS_TO_EXTRACT:
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if field in FIELDS_TO_SUFFIX:
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filtered[f"{field}_{suffix}"] = row.get(field, "")
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elif field in KEY_COLUMNS:
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filtered[field] = row.get(field, "")
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else:
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if field not in data.get(key, {}):
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filtered[field] = row.get(field, "")
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if key not in data:
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data[key] = filtered
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else:
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data[key].update(filtered)
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return data
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def merge_dicts_by_key(dicts):
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"""Merge all dicts on shared key."""
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merged = defaultdict(dict)
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for d in dicts:
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for key, row in d.items():
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merged[key].update(row)
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return merged
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def write_merged_csv(merged_data, output_file):
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"""Write merged dictionary to CSV."""
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sorted_keys = sorted(merged_data.keys(), key=lambda x: (x[0], int(x[1])))
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# Determine full set of columns
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all_fields = set()
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for row in merged_data.values():
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all_fields.update(row.keys())
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# Reorder fields: key columns first, then others
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fieldnames = KEY_COLUMNS + sorted(all_fields - set(KEY_COLUMNS))
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with open(output_file, 'w', newline='') as f:
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writer = csv.DictWriter(f, fieldnames=fieldnames)
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writer.writeheader()
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for key in sorted_keys:
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writer.writerow(merged_data[key])
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def main():
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parser = argparse.ArgumentParser(
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description="Merge TP/FP/FN CSVs by CHROM,POS,tag, keep selected fields, and suffix REF/ALT from filename."
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)
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parser.add_argument("files", nargs='+', help="Input CSV files (e.g. *_TP.csv)")
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parser.add_argument("--output", required=True, help="Output merged CSV file")
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args = parser.parse_args()
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all_dicts = []
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for file in args.files:
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suffix = extract_sample_suffix(file)
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print(f"Processing {file} (sample: {suffix})")
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sample_dict = load_csv_by_key(file, suffix)
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all_dicts.append(sample_dict)
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merged = merge_dicts_by_key(all_dicts)
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write_merged_csv(merged, args.output)
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print(f"Merged CSV written to {args.output}")
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if __name__ == "__main__":
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main()

‎bin/split_sompy_features.py‎

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#!/usr/bin/env python
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# Copyright 2025 - GHGA
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# Author: Kuebra Narci - @kubranarci
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'''
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Generates a CSV file from a VCF
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Expected usage:
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$ python split_sompy_features.py <vcf_file> <prefix>
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Use --help for more information.
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'''
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import csv
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import argparse
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import os
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def split_csv_by_tag(input_file, prefix):
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output_files = {
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'TP': f'{prefix}_TP.csv',
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'FP': f'{prefix}_FP.csv',
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'FN': f'{prefix}_FN.csv'
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}
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try:
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with open(input_file, newline='') as infile:
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reader = csv.reader(infile)
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header = next(reader)
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# Prepare output writers
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writers = {}
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files = {}
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for tag, filename in output_files.items():
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f = open(filename, 'w', newline='')
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writer = csv.writer(f)
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writer.writerow(header)
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writers[tag] = writer
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files[tag] = f
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# Write rows to correct files
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for row in reader:
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if len(row) > 3:
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tag = row[3]
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if tag in writers:
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writers[tag].writerow(row)
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# Close all output files
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for f in files.values():
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f.close()
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print("Done. Files created:")
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for filename in output_files.values():
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print(f" - {filename}")
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except FileNotFoundError:
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print(f"Error: File '{input_file}' not found.")
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except Exception as e:
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print(f"An error occurred: {e}")
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def main():
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parser = argparse.ArgumentParser(description="Split a CSV file into TP, FP, and FN files based on the 'tag' column.")
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parser.add_argument("input_csv", help="Path to the input CSV file")
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parser.add_argument("prefix", help="Path to the input CSV file")
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args = parser.parse_args()
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split_csv_by_tag(args.input_csv, args.prefix)
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if __name__ == "__main__":
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main()

‎conf/modules.config‎

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@@ -316,14 +316,20 @@ process {
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317317
withName: "HAPPY_SOMPY" {
318318
ext.prefix = {"${meta.id}.${params.truth_id}.${meta.caller}"}
319-
ext.args = { meta.caller.contains("strelka") || meta.caller.contains("varscan") || meta.caller.contains("pisces") ? "--feature-table hcc.${meta.caller}.${params.variant_type} --bin-afs" : "--feature-table generic" }
319+
ext.args = { meta.caller.contains("strelka") || meta.caller.contains("varscan") || meta.caller.contains("pisces") || meta.caller == "mutect" ? "--feature-table hcc.${meta.caller}.${params.variant_type} --bin-afs" : "--feature-table generic" }
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publishDir = [
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path: {"${params.outdir}/${params.variant_type}/${meta.id}/benchmarks/sompy"},
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pattern: "*{.csv.gz,csv,json.gz,json,vcf.gz,vcf.gz.tbi,csv}",
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mode: params.publish_dir_mode
324324
]
325325
}
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327+
withName: "SPLIT_SOMPY_FEATURES" {
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publishDir = [
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enabled: false
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]
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}
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327333
withName: "HAPPY_PREPY" {
328334
ext.prefix = {"${meta.id}.${params.truth_id}.${meta.caller}.prepy"}
329335
ext.args = {"--fixchr --filter-nonref --bcftools-norm"}
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471477
withName: VCF_TO_CSV {
472478
ext.prefix = {"${meta.id}.${meta.tag}"}
473479
publishDir = [
474-
path: {"${params.outdir}/${params.variant_type}/summary/comparisons/"},
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path: {"${params.outdir}/${params.variant_type}/summary/comparisons/${meta.id}"},
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pattern: "*{.csv}",
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mode: params.publish_dir_mode
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]
478484
}
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486+
withName: MERGE_SOMPY_FEATURES {
487+
publishDir = [
488+
path: {"${params.outdir}/${params.variant_type}/summary/comparisons/${meta.id}"},
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pattern: "*{csv}",
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mode: params.publish_dir_mode
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]
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}
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// VCF2BED tools
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withName: "SVTK_VCF2BED" {

‎modules/local/custom/merge_sompy_features/environment.yml‎

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channels:
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- conda-forge
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- bioconda
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dependencies:
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- pip
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- pip:
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- pandas==2.2.3

‎modules/local/custom/merge_sompy_features/main.nf‎

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process MERGE_SOMPY_FEATURES {
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tag "$meta.id"
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label 'process_single'
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ab/ab3b0054e3111812d8f2deb12345d5b7ca7ea7b18a2dbcbf174d46274c28deba/data':
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'community.wave.seqera.io/library/pip_pandas:40d2e76c16c136f0' }"
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input:
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tuple val(meta), path(csvs)
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output:
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tuple val(meta), path("*.summary.csv") , emit: TP
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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merge_sompy_features.py $csvs --output ${prefix}.${meta.tag}.summary.csv
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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python: \$(python --version | sed 's/Python //g')
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.${meta.tag}.summary.csv
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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python: \$(python --version | sed 's/Python //g')
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END_VERSIONS
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"""
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}

‎modules/local/custom/split_sompy_features/environment.yml‎

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channels:
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- conda-forge
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- bioconda
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dependencies:
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- pip
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- pip:
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- pandas==2.2.3

‎modules/local/custom/split_sompy_features/main.nf‎

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process SPLIT_SOMPY_FEATURES {
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tag "$meta.id"
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label 'process_single'
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ab/ab3b0054e3111812d8f2deb12345d5b7ca7ea7b18a2dbcbf174d46274c28deba/data':
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'community.wave.seqera.io/library/pip_pandas:40d2e76c16c136f0' }"
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input:
11+
tuple val(meta), path(input)
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output:
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tuple val(meta), path("*TP.csv") , emit: TP
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tuple val(meta), path("*FP.csv") , emit: FP
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tuple val(meta), path("*FN.csv") , emit: FN
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path "versions.yml" , emit: versions
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when:
20+
task.ext.when == null || task.ext.when
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22+
script:
23+
def args = task.ext.args ?: ''
24+
def prefix = task.ext.prefix ?: "${meta.id}"
25+
26+
"""
27+
split_sompy_features.py $input $prefix
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cat <<-END_VERSIONS > versions.yml
29+
"${task.process}":
30+
python: \$(python --version | sed 's/Python //g')
31+
END_VERSIONS
32+
"""
33+
stub:
34+
def prefix = task.ext.prefix ?: "${meta.id}"
35+
"""
36+
touch ${prefix}_TP.csv
37+
touch ${prefix}_FP.csv
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touch ${prefix}_FN.csv
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cat <<-END_VERSIONS > versions.yml
41+
"${task.process}":
42+
python: \$(python --version | sed 's/Python //g')
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END_VERSIONS
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"""
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}

‎subworkflows/local/compare_benchmark_results/main.nf‎

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33
// COMPARE_BENCHMARK_RESULTS: SUBWORKFLOW to merge TP/FP/FN results from different tools.
44
//
55

6-
include { SURVIVOR_MERGE } from '../../../modules/nf-core/survivor/merge'
7-
include { BCFTOOLS_MERGE } from '../../../modules/nf-core/bcftools/merge'
8-
include { VCF_TO_CSV } from '../../../modules/local/custom/vcf_to_csv'
9-
include { REFORMAT_HEADER } from '../../../modules/local/custom/reformat_header'
6+
include { SURVIVOR_MERGE } from '../../../modules/nf-core/survivor/merge'
7+
include { BCFTOOLS_MERGE } from '../../../modules/nf-core/bcftools/merge'
8+
include { VCF_TO_CSV } from '../../../modules/local/custom/vcf_to_csv'
9+
include { REFORMAT_HEADER } from '../../../modules/local/custom/reformat_header'
10+
include { MERGE_SOMPY_FEATURES } from '../../../modules/local/custom/merge_sompy_features'
1011
include { TABIX_BGZIP as TABIX_BGZIP_UNZIP } from '../../../modules/nf-core/tabix/bgzip'
1112

1213
workflow COMPARE_BENCHMARK_RESULTS {
1314
take:
14-
evaluations // channel: [val(meta), vcf.gz, index]
15-
fasta // reference channel [val(meta), ref.fa]
16-
fai // reference channel [val(meta), ref.fa.fai]
15+
evaluations // channel: [val(meta), vcf.gz, index]
16+
evaluations_csv // channel: [val(meta), csv]
17+
fasta // reference channel [val(meta), ref.fa]
18+
fai // reference channel [val(meta), ref.fa.fai]
1719

1820
main:
1921
versions = Channel.empty()
@@ -69,6 +71,12 @@ workflow COMPARE_BENCHMARK_RESULTS {
6971
)
7072
versions = versions.mix(VCF_TO_CSV.out.versions.first())
7173

74+
75+
MERGE_SOMPY_FEATURES(
76+
evaluations_csv.groupTuple()
77+
)
78+
versions = versions.mix(MERGE_SOMPY_FEATURES.out.versions.first())
79+
7280
emit:
7381
merged_vcfs // channel: [val(meta), vcf]
7482
versions // channel: [versions.yml]

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