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fix: for asseess_genome_creation when there are no variants #44

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Merged
mcolpus merged 1 commit into from
May 18, 2026
Merged

fix: for asseess_genome_creation when there are no variants #44

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6 changes: 5 additions & 1 deletion CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,6 +1,10 @@
## 1.1.2

- fix for assess_genome_creation when vcf tables is empty

## 1.1.1

- fix for asseess_genome_creation when there are no indels
- fix for assess_genome_creation when there are no indels

## 1.1.0

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2 changes: 1 addition & 1 deletion Cargo.lock
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2 changes: 1 addition & 1 deletion Cargo.toml
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@@ -1,6 +1,6 @@
[package]
name = "rundial"
version = "1.1.1"
version = "1.1.2"
edition = "2024"
rust-version = "1.93"

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8 changes: 4 additions & 4 deletions process/consensus.nf
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@@ -1,7 +1,7 @@
process apply_filters {
publishDir "${params.publish_dir}", enabled: params.publish_dir != "", mode: "copy", saveAs: { filename -> sample_name + "." + filename }
container {
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.1' : params.test_container_rundial
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.2' : params.test_container_rundial
}
cpus 1

Expand Down Expand Up @@ -29,7 +29,7 @@ process apply_filters {
process make_consensus {
publishDir "${params.publish_dir}", enabled: params.publish_dir != "", mode: "copy", saveAs: { filename -> sample_name + "." + filename }
container {
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.1' : params.test_container_rundial
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.2' : params.test_container_rundial
}
cpus 1
memory "4 GB"
Expand Down Expand Up @@ -75,7 +75,7 @@ process make_consensus {
process make_clair3_consensus {
publishDir "${params.publish_dir}", enabled: params.publish_dir != "", mode: "copy", saveAs: { filename -> sample_name + "." + filename }
container {
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.1' : params.test_container_rundial
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.2' : params.test_container_rundial
}
cpus 1
memory "3 GB"
Expand Down Expand Up @@ -123,7 +123,7 @@ process make_clair3_consensus {
process reassess_genome_creation {
publishDir "${params.publish_dir}", enabled: params.publish_dir != "", mode: "copy", saveAs: { filename -> sample_name + "." + filename }
container {
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.1' : params.test_container_rundial
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.2' : params.test_container_rundial
}
cpus 1

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10 changes: 5 additions & 5 deletions process/variant_calling.nf
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Expand Up @@ -3,7 +3,7 @@ params.test_cpus = ""
process minimap2 {
publishDir "${params.publish_dir}", enabled: params.publish_dir != "", mode: "copy", saveAs: { filename -> sample_name + "." + filename }
container {
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.1' : params.test_container_rundial
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.2' : params.test_container_rundial
}
cpus {
params.testing == "" ? 4 : params.test_cpus
Expand Down Expand Up @@ -32,7 +32,7 @@ process minimap2 {
process call_snps {
publishDir "${params.publish_dir}", enabled: params.publish_dir != "", mode: "copy", saveAs: { filename -> sample_name + "." + filename }
container {
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.1' : params.test_container_rundial
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.2' : params.test_container_rundial
}
cpus {
params.testing == "" ? 4 : params.test_cpus
Expand Down Expand Up @@ -78,7 +78,7 @@ process call_snps {
process call_all {
publishDir "${params.publish_dir}", enabled: params.publish_dir != "", mode: "copy", saveAs: { filename -> sample_name + "." + filename }
container {
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.1' : params.test_container_rundial
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.2' : params.test_container_rundial
}
cpus {
params.testing == "" ? 4 : params.test_cpus
Expand Down Expand Up @@ -132,7 +132,7 @@ process call_all {

process get_clair3_model {
container {
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.1' : params.test_container_rundial
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.2' : params.test_container_rundial
}

pod label: "name", value: "rundial:get_clair3_model"
Expand All @@ -155,7 +155,7 @@ process get_clair3_model {
process clair3 {
publishDir "${params.publish_dir}", enabled: params.publish_dir != "", mode: "copy", saveAs: { filename -> sample_name + "." + filename }
container {
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.1' : params.test_container_rundial
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.2' : params.test_container_rundial
}
cpus {
params.testing == "" ? 4 : params.test_cpus
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4 changes: 2 additions & 2 deletions pyproject.toml
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Expand Up @@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"

[project]
name = "rundial"
version = "1.1.1"
version = "1.1.2"
description = "Reference based assembly of ONT reads."
classifiers = [
"Environment :: Console",
Expand Down Expand Up @@ -37,7 +37,7 @@ version_scheme = "semver"
version_provider = "pep621"

[tool.version_bumper]
active_version = "1.1.1"
active_version = "1.1.2"
version_files = [
"process/variant_calling.nf",
"process/consensus.nf",
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18 changes: 13 additions & 5 deletions src/helper_scripts/assess_genome_creation.py
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Expand Up @@ -203,9 +203,14 @@ def get_depths(row) -> tuple[list[int] | None, list[int] | None, list[int], int]
f"Could not find suitable depth fields for row with FORMAT {row['FORMAT']}.\nrow={row}"
)

vcf[["ADF", "ADR", "COV", "HQ_DP"]] = vcf.apply(
get_depths, axis=1, result_type="expand"
)
if vcf.empty:
vcf[["ADF", "ADR", "COV", "HQ_DP"]] = pd.DataFrame(
[[None, None, [0], 0]], index=vcf.index
)
else:
vcf[["ADF", "ADR", "COV", "HQ_DP"]] = vcf.apply(
get_depths, axis=1, result_type="expand"
)
return vcf


Expand Down Expand Up @@ -239,7 +244,10 @@ def is_het(row) -> bool:
return False
return True

vcf["is_het"] = vcf.apply(is_het, axis=1)
if vcf.empty:
vcf["is_het"] = False
else:
vcf["is_het"] = vcf.apply(is_het, axis=1)
return vcf


Expand Down Expand Up @@ -267,7 +275,7 @@ def in_mask(contig, pos, mask_set, ref):

mask_set = set(zip(mask["contig"], mask["position"]))

if mask_set:
if mask_set and not vcf.empty:
vcf["is_masked"] = vcf.apply(
lambda row: in_mask(row["CHROM"], row["POS"], mask_set, row["REF"]), axis=1
)
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2 changes: 1 addition & 1 deletion test_data/clair3_consensus/expected.vcf
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@@ -1,5 +1,5 @@
##fileformat=VCFv4.2
##rundial_consensus_version=1.1.1
##rundial_consensus_version=1.1.2
##FILTER=<ID=LowQual,Description="Low quality variant">
##FILTER=<ID=RefCall,Description="Reference call">
##FILTER=<ID=PASS,Description="All filters passed">
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2 changes: 1 addition & 1 deletion test_data/single_consensus/expected.vcf
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@@ -1,5 +1,5 @@
##fileformat=VCFv4.2
##rundial_consensus_version=1.1.1
##rundial_consensus_version=1.1.2
##FILTER=<ID=INVALID_INDEL,Description="Call is indel but has no ALT alleles.">
##FILTER=<ID=LOW_HQ_DEPTH,Description="High quality depth is less than 5">
##FILTER=<ID=LOW_MQ,Description="Mapping Quality. MQ is less than 30">
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2 changes: 1 addition & 1 deletion test_data/support_consensus/expected.vcf
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@@ -1,5 +1,5 @@
##fileformat=VCFv4.2
##rundial_consensus_version=1.1.1
##rundial_consensus_version=1.1.2
##FILTER=<ID=INVALID_INDEL,Description="Call is indel but has no ALT alleles.">
##FILTER=<ID=LOW_HQ_DEPTH,Description="High quality depth is less than 5">
##FILTER=<ID=LOW_MQ,Description="Mapping Quality. MQ is less than 30">
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2 changes: 1 addition & 1 deletion test_data/write_vcf.vcf
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@@ -1,5 +1,5 @@
##fileformat=VCFv4.2
##rundial_consensus_version=1.1.1
##rundial_consensus_version=1.1.2
##FILTER=<ID=INVALID_INDEL,Description="Call is indel but has no ALT alleles.">
##FILTER=<ID=LOW_HQ_DEPTH,Description="High quality depth is less than 5">
##FILTER=<ID=LOW_MQ,Description="Mapping Quality. MQ is less than 30">
Expand Down
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