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fix: stop pushing to gpasltd #45

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Merged
mcolpus merged 1 commit into from
May 19, 2026
Merged

fix: stop pushing to gpasltd #45

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23 changes: 0 additions & 23 deletions .github/workflows/build_and_push_container.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,6 @@ on:
env:
REGISTRY: lhr.ocir.io
IMAGE_NAME: lrbvkel2wjot/gpas/rundial
IMAGE_NAME_GPAS_LTD: lr3yhdniv6gu/gpas/rundial

jobs:
build:
Expand Down Expand Up @@ -64,25 +63,3 @@ jobs:
file: Dockerfile
tags: |
${{ env.RUNDIAL_TAG }}

- name: Login to gpasltd OCIR
uses: docker/login-action@v3
with:
registry: ${{ env.REGISTRY }}
username: ${{ secrets.OCR_CONTAINER_USERNAME_GPASLTD }}
password: ${{ secrets.OCR_CONTAINER_TOKEN_GPASLTD }}

- name: Set full image registry tag for gpasltd
run: |
echo "RUNDIAL_TAG=${{ env.REGISTRY }}/${{ env.IMAGE_NAME_GPAS_LTD }}:${{ env.tag }}" >> $GITHUB_ENV
echo "RUNDIAL_TAG: ${{ env.RUNDIAL_TAG }}"

- name: Build and push
id: build_and_push_gpasltd
uses: docker/build-push-action@v4
with:
context: .
push: true
file: Dockerfile
tags: |
${{ env.RUNDIAL_TAG }}
4 changes: 4 additions & 0 deletions CHANGELOG.md
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@@ -1,3 +1,7 @@
## 1.1.3

- stop pushing to gpasltd

## 1.1.2

- fix for assess_genome_creation when vcf tables is empty
Expand Down
2 changes: 1 addition & 1 deletion Cargo.lock
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2 changes: 1 addition & 1 deletion Cargo.toml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[package]
name = "rundial"
version = "1.1.2"
version = "1.1.3"
edition = "2024"
rust-version = "1.93"

Expand Down
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:1.1.2' : params.test_container_rundial
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.3' : params.test_container_rundial
}
cpus 1

Expand Down Expand Up @@ -29,7 +29,7 @@ process apply_filters {
process make_consensus {
publishDir "${params.publish_dir}", enabled: params.publish_dir != "", mode: "copy", saveAs: { filename -> sample_name + "." + filename }
container {
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.2' : params.test_container_rundial
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.3' : params.test_container_rundial
}
cpus 1
memory "4 GB"
Expand Down Expand Up @@ -75,7 +75,7 @@ process make_consensus {
process make_clair3_consensus {
publishDir "${params.publish_dir}", enabled: params.publish_dir != "", mode: "copy", saveAs: { filename -> sample_name + "." + filename }
container {
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.2' : params.test_container_rundial
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.3' : 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:1.1.2' : params.test_container_rundial
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.3' : params.test_container_rundial
}
cpus 1

Expand Down
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 "${params.publish_dir}", enabled: params.publish_dir != "", mode: "copy", saveAs: { filename -> sample_name + "." + filename }
container {
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.2' : params.test_container_rundial
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.3' : params.test_container_rundial
}
cpus {
params.testing == "" ? 4 : params.test_cpus
Expand Down Expand Up @@ -32,7 +32,7 @@ process minimap2 {
process call_snps {
publishDir "${params.publish_dir}", enabled: params.publish_dir != "", mode: "copy", saveAs: { filename -> sample_name + "." + filename }
container {
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.2' : params.test_container_rundial
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.3' : 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:1.1.2' : params.test_container_rundial
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.3' : 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:1.1.2' : params.test_container_rundial
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.3' : 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:1.1.2' : params.test_container_rundial
params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.3' : params.test_container_rundial
}
cpus {
params.testing == "" ? 4 : params.test_cpus
Expand Down
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 = "1.1.2"
version = "1.1.3"
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 = "1.1.2"
active_version = "1.1.3"
version_files = [
"process/variant_calling.nf",
"process/consensus.nf",
Expand Down
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=1.1.2
##rundial_consensus_version=1.1.3
##FILTER=<ID=LowQual,Description="Low quality variant">
##FILTER=<ID=RefCall,Description="Reference call">
##FILTER=<ID=PASS,Description="All filters passed">
Expand Down
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=1.1.2
##rundial_consensus_version=1.1.3
##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
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=1.1.2
##rundial_consensus_version=1.1.3
##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
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=1.1.2
##rundial_consensus_version=1.1.3
##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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