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Simplify reference handling through the workflow prepareAnnotation [CW-7232]

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This commit is contained in:
Natalia Garcia 2026-05-20 12:49:08 +00:00
parent 3e9d57a9e1
commit dc0ebf3a52
4 changed files with 19 additions and 41 deletions
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27
bin/workflow_glue/prepare_annotation_reference.py
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@ -51,33 +51,17 @@ def _find_patterns(text, patterns):
class PreparedReference:
"""A reference genome prepared for analysis."""
def __init__(self, input_path, work_dir):
def __init__(self, input_path):
"""Initialize and prepare reference genome."""
self.input_path = Path(input_path)
self.work_dir = Path(work_dir)
self.output_path = self.work_dir / "reference.fasta"
self._seqnames = None
self._prepare()
def _prepare(self):
"""Prepare reference (decompress if gzipped)."""
if _is_gzip(self.input_path):
with gzip.open(self.input_path, "rb") as src, open(
self.output_path, "wb"
) as dst:
shutil.copyfileobj(src, dst)
else:
shutil.copyfile(self.input_path, self.output_path)
if not self.output_path.exists() or self.output_path.stat().st_size < 1:
raise ValueError(f"Prepared file is empty: {self.output_path}")
@property
def seqnames(self):
"""Extract and cache sorted FASTA sequence names."""
if self._seqnames is None:
ids = set()
with open(self.output_path, encoding="utf-8") as f:
with open(self.input_path, encoding="utf-8") as f:
for line in f:
if line.startswith(">"):
ids.add(line[1:].split()[0])
@ -94,7 +78,7 @@ class PreparedReference:
providers.update(_find_patterns(self.input_path.name, PROVIDER_PATTERNS))
# check headers
with open(self.output_path, encoding="utf-8") as f:
with open(self.input_path, encoding="utf-8") as f:
for line in f:
if line.startswith(">"):
builds.update(_find_patterns(line, BUILD_PATTERNS))
@ -475,7 +459,7 @@ def prepare_annotation_reference(annotation, reference, out_dir):
out_dir.mkdir(parents=True, exist_ok=False)
# prepare reference genome
ref = PreparedReference(reference, out_dir)
ref = PreparedReference(reference)
# prepare annotation (convert to GTF if needed, then filter to stranded)
ann = Annotation(annotation, out_dir)
@ -518,7 +502,6 @@ def prepare_annotation_reference(annotation, reference, out_dir):
},
"reference": {
"input": str(ref.input_path),
"prepared": str(ref.output_path),
},
"seqnames": seqnames,
"analysis_seqnames": seqnames,
@ -555,7 +538,7 @@ def main(args):
logger.info(
"Prepared annotation %s and reference %s.",
summary["annotation"]["prepared"],
summary["reference"]["prepared"],
summary["reference"]["input"],
)

17
bin/workflow_glue/tests/wf/test_prepare_annotation_reference.py
View File

@ -73,11 +73,11 @@ MOUSE_GTF = (
[
(SIMPLE_REFERENCE, "reference.fa", SIMPLE_GTF,
"annotation.gtf"),
(SIMPLE_REFERENCE, "reference.fa.gz", SIMPLE_GTF,
(SIMPLE_REFERENCE, "reference.fa", SIMPLE_GTF,
"annotation.gtf.gz"),
(SIMPLE_REFERENCE, "reference.fa", GFF3_INPUT,
"annotation.gff3.gz"),
(NCBI_REFERENCE, "reference.fna.gz", NCBI_GTF,
(NCBI_REFERENCE, "reference.fna", NCBI_GTF,
"annotation.gtf.gz"),
(SIMPLE_REFERENCE + ">chrExtra\nTTTT\n", "reference.fa",
MIXED_STRANDED_GTF, "annotation.gtf"),
@ -94,10 +94,7 @@ def test_prepare_all_formats_produce_valid_outputs(
"""All supported input formats produce annotation.gtf and reference.fasta."""
# write reference
ref_path = tmp_path / ref_name
if ref_name.endswith(".gz"):
_write_gzip(ref_path, ref_data)
else:
_write(ref_path, ref_data)
_write(ref_path, ref_data)
# write annotation
annot_path = tmp_path / annot_name
@ -113,15 +110,15 @@ def test_prepare_all_formats_produce_valid_outputs(
# output files must exist
assert (out_dir / "annotation.gtf").exists()
assert (out_dir / "reference.fasta").exists()
assert (ref_path).exists()
assert (out_dir / "annotation_reference_summary.json").exists()
# paths returned in summary must match
assert summary["annotation"]["prepared"] == str(out_dir / "annotation.gtf")
assert summary["reference"]["prepared"] == str(out_dir / "reference.fasta")
assert summary["reference"]["input"] == str(ref_path)
# outputs must be valid for downstream tools (Bambu, SQANTI)
reference = Path(summary["reference"]["prepared"])
reference = Path(summary["reference"]["input"])
annotation = Path(summary["annotation"]["prepared"])
assert reference.read_text(encoding="utf-8").startswith(">")
assert summary["analysis_seqnames"]["has_overlap"] is True
@ -142,7 +139,7 @@ def test_prepare_all_formats_produce_valid_outputs(
def test_ncbi_format_sanitises_gene_ids(tmp_path):
"""NCBI gene_id='transcript_id' should be sanitised to actual transcript_id."""
reference = _write_gzip(tmp_path / "reference.fna.gz", NCBI_REFERENCE)
reference = _write(tmp_path / "reference.fna", NCBI_REFERENCE)
annotation = _write_gzip(tmp_path / "annotation.gtf.gz", NCBI_GTF)
summary = prepare_annotation_reference.prepare_annotation_reference(

4
modules/local/bambu_chunked.nf
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@ -14,7 +14,7 @@ process bambuDiscover {
input:
tuple val(meta), val(aliases), path(bams, stageAs: "bams/??.bam"), path(bais, stageAs: "bams/??.bam.bai"), path(sample_sheet)
path annotation, stageAs: "annotation/*"
path reference, stageAs: "reference/*"
tuple path(reference, stageAs: "reference/reference.fa"), path(ref_fai, stageAs: "reference/reference.fai")
output:
tuple val(meta), path("discover"), emit: dir
script:
@ -51,7 +51,7 @@ process bambuQuant {
errorStrategy 'retry'
input:
tuple val(meta), val(chunk_id), val(annotation_tx_count), path(chunk_rds), path(discovered_annotation)
path reference, stageAs: "reference/*"
tuple path(reference, stageAs: "reference/reference.fa"), path(ref_fai, stageAs: "reference/reference.fai")
output:
tuple val(meta), val(chunk_id), path("${chunk_id}"), emit: dir
script:

12
subworkflows/transcriptome.nf
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@ -91,7 +91,6 @@ process prepareAnnotationReference {
output:
stdout emit: warnings
path "annotation.gtf", emit: annotation
path "reference.fasta", emit: reference
path "annotation_reference_summary.json", emit: summary
path "unstranded_annotation.gtf", optional: true, emit: unstranded
script:
@ -111,7 +110,7 @@ process buildCohortTranscriptomeFasta {
memory "4 GB"
input:
path "transcripts.gtf"
path reference
tuple path(reference), path(ref_idx)
output:
path "cohort.transcriptome.fa", emit: fasta
script:
@ -127,7 +126,7 @@ process buildSampleTranscriptomeFasta {
memory "4 GB"
input:
tuple val(meta), path("transcripts.gtf")
path reference
tuple path(reference), path(ref_idx)
output:
tuple val(meta), path("${meta.alias}.transcriptome.fa"), emit: fasta
script:
@ -144,7 +143,7 @@ process runJointSqanti {
input:
path gtf
path annotation, stageAs: "annotation/*"
path reference, stageAs: "reference/*"
tuple path(reference, stageAs: "reference/reference.fa"), path(ref_fai, stageAs: "reference/reference.fai")
output:
path "sqanti_cohort", emit: dir
path "sqanti_cohort/classification_summary.tsv", emit: summary
@ -177,7 +176,7 @@ process runPerSampleSqanti {
input:
tuple val(meta), path(gtf)
path annotation, stageAs: "annotation/*"
path reference, stageAs: "reference/*"
tuple path(reference, stageAs: "reference/reference.fa"), path(ref_fai, stageAs: "reference/reference.fai")
output:
tuple val(meta), path("${meta.alias}_sqanti"), emit: dir
tuple val(meta), path("${meta.alias}_sqanti/classification_summary.tsv"), emit: summary
@ -217,8 +216,7 @@ workflow transcriptome_analysis {
}
}
analysis_annotation = prepared_reference_annotation.annotation.first()
analysis_reference = prepared_reference_annotation.reference.first()
analysis_reference = ref_genome.first()
joint_meta = [alias: "cohort"]
joint_discover = runJointBambuDiscover(