diff --git a/.github/workflows/build_and_push_container.yml b/.github/workflows/build_and_push_container.yml index a4ba07b..9f859a6 100644 --- a/.github/workflows/build_and_push_container.yml +++ b/.github/workflows/build_and_push_container.yml @@ -15,7 +15,6 @@ on: env: REGISTRY: lhr.ocir.io IMAGE_NAME: lrbvkel2wjot/gpas/rundial - IMAGE_NAME_GPAS_LTD: lr3yhdniv6gu/gpas/rundial jobs: build: @@ -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: | - ${{ env.RUNDIAL_TAG }} diff --git a/CHANGELOG.md b/CHANGELOG.md index 1b94306..571712e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,7 @@ +## 1.1.3 + +- stop pushing to gpasltd + ## 1.1.2 - fix for assess_genome_creation when vcf tables is empty diff --git a/Cargo.lock b/Cargo.lock index 2003477..24c5f9d 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -653,7 +653,7 @@ checksum = "dc897dd8d9e8bd1ed8cdad82b5966c3e0ecae09fb1907d58efaa013543185d0a" [[package]] name = "rundial" -version = "1.1.2" +version = "1.1.3" dependencies = [ "clap", "indexmap", diff --git a/Cargo.toml b/Cargo.toml index b6f5354..029c5e8 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "rundial" -version = "1.1.2" +version = "1.1.3" edition = "2024" rust-version = "1.93" diff --git a/process/consensus.nf b/process/consensus.nf index b690001..cdc25dd 100644 --- a/process/consensus.nf +++ b/process/consensus.nf @@ -1,7 +1,7 @@ process apply_filters { publishDir "${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 @@ -29,7 +29,7 @@ process apply_filters { process make_consensus { publishDir "${params.publish_dir}", enabled: params.publish_dir != "", mode: "copy", saveAs: { filename -> sample_name + "." + filename } container { - params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.2' : params.test_container_rundial + params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.3' : params.test_container_rundial } cpus 1 memory "4 GB" @@ -75,7 +75,7 @@ process make_consensus { process make_clair3_consensus { publishDir "${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" @@ -123,7 +123,7 @@ process make_clair3_consensus { process reassess_genome_creation { publishDir "${params.publish_dir}", enabled: params.publish_dir != "", mode: "copy", saveAs: { filename -> sample_name + "." + filename } container { - params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.2' : params.test_container_rundial + params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.3' : params.test_container_rundial } cpus 1 diff --git a/process/variant_calling.nf b/process/variant_calling.nf index ebb8a3c..8fb56b3 100644 --- a/process/variant_calling.nf +++ b/process/variant_calling.nf @@ -3,7 +3,7 @@ params.test_cpus = "" process minimap2 { publishDir "${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 @@ -32,7 +32,7 @@ process minimap2 { process call_snps { publishDir "${params.publish_dir}", enabled: params.publish_dir != "", mode: "copy", saveAs: { filename -> sample_name + "." + filename } container { - params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.2' : params.test_container_rundial + params.test_container_rundial == "" ? params.container_prefix + '/gpas/rundial:1.1.3' : params.test_container_rundial } cpus { params.testing == "" ? 4 : params.test_cpus @@ -78,7 +78,7 @@ process call_snps { process call_all { publishDir "${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 @@ -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" @@ -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 diff --git a/pyproject.toml b/pyproject.toml index c8d44c7..565a692 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -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", @@ -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", diff --git a/test_data/clair3_consensus/expected.vcf b/test_data/clair3_consensus/expected.vcf index 4fd7423..5861636 100644 --- a/test_data/clair3_consensus/expected.vcf +++ b/test_data/clair3_consensus/expected.vcf @@ -1,5 +1,5 @@ ##fileformat=VCFv4.2 -##rundial_consensus_version=1.1.2 +##rundial_consensus_version=1.1.3 ##FILTER= ##FILTER= ##FILTER= diff --git a/test_data/single_consensus/expected.vcf b/test_data/single_consensus/expected.vcf index a58c11f..2d3d939 100644 --- a/test_data/single_consensus/expected.vcf +++ b/test_data/single_consensus/expected.vcf @@ -1,5 +1,5 @@ ##fileformat=VCFv4.2 -##rundial_consensus_version=1.1.2 +##rundial_consensus_version=1.1.3 ##FILTER= ##FILTER= ##FILTER= diff --git a/test_data/support_consensus/expected.vcf b/test_data/support_consensus/expected.vcf index f166cd1..2a3fdf3 100644 --- a/test_data/support_consensus/expected.vcf +++ b/test_data/support_consensus/expected.vcf @@ -1,5 +1,5 @@ ##fileformat=VCFv4.2 -##rundial_consensus_version=1.1.2 +##rundial_consensus_version=1.1.3 ##FILTER= ##FILTER= ##FILTER= diff --git a/test_data/write_vcf.vcf b/test_data/write_vcf.vcf index 018e1ae..fc7f88a 100644 --- a/test_data/write_vcf.vcf +++ b/test_data/write_vcf.vcf @@ -1,5 +1,5 @@ ##fileformat=VCFv4.2 -##rundial_consensus_version=1.1.2 +##rundial_consensus_version=1.1.3 ##FILTER= ##FILTER= ##FILTER=