diff --git a/.github/workflows/docker.yaml b/.github/workflows/docker.yaml index 2a8d2d0..87e9861 100644 --- a/.github/workflows/docker.yaml +++ b/.github/workflows/docker.yaml @@ -15,7 +15,7 @@ on: permissions: {} env: - VERSION: 0.1.6 + VERSION: 0.1.7 IMAGE_NAME: cpg-flow-seqr-loader DOCKER_DEV: australia-southeast1-docker.pkg.dev/cpg-common/images-dev DOCKER_MAIN: australia-southeast1-docker.pkg.dev/cpg-common/images diff --git a/README.md b/README.md index 91ecc94..604739d 100644 --- a/README.md +++ b/README.md @@ -55,7 +55,7 @@ CPG-Flow workflows are operated entirely by defining input Cohorts (see [here](h ```bash analysis-runner \ --skip-repo-checkout \ - --image australia-southeast1-docker.pkg.dev/cpg-common/images/cpg-flow-seqr-loader:0.1.6 \ + --image australia-southeast1-docker.pkg.dev/cpg-common/images/cpg-flow-seqr-loader:0.1.7 \ --config src/cpg_seqr_loader/config_template.toml \ --config cohorts.toml \ # containing the inputs_cohorts and sequencing_type --dataset seqr \ @@ -70,7 +70,7 @@ analysis-runner \ ```bash analysis-runner \ --skip-repo-checkout \ - --image australia-southeast1-docker.pkg.dev/cpg-common/images/cpg-flow-seqr-loader:0.1.6 \ + --image australia-southeast1-docker.pkg.dev/cpg-common/images/cpg-flow-seqr-loader:0.1.7 \ --config src/cpg_seqr_loader/config_template.toml \ --config cohorts.toml \ # containing the inputs_cohorts and sequencing_type --dataset seqr \ diff --git a/pyproject.toml b/pyproject.toml index c9d7a5d..faf2fbd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,7 +8,7 @@ description='Seqr-Loader (gVCF-combiner) implemented in CPG-Flow' readme = "README.md" # currently cpg-flow is pinned to this version requires-python = ">=3.10,<3.11" -version="0.1.6" +version="0.1.7" license={"file" = "LICENSE"} classifiers=[ 'Environment :: Console', @@ -122,7 +122,7 @@ hail = ["hail"] "src/cpg_seqr_loader/scripts/annotate_cohort.py" = ["E501"] [tool.bumpversion] -current_version = "0.1.6" +current_version = "0.1.7" parse = "(?P\\d+)\\.(?P\\d+)\\.(?P\\d+)" serialize = ["{major}.{minor}.{patch}"] commit = true diff --git a/src/cpg_seqr_loader/jobs/CombineGvcfsIntoVds.py b/src/cpg_seqr_loader/jobs/CombineGvcfsIntoVds.py index 4a3767b..34d877b 100644 --- a/src/cpg_seqr_loader/jobs/CombineGvcfsIntoVds.py +++ b/src/cpg_seqr_loader/jobs/CombineGvcfsIntoVds.py @@ -3,7 +3,7 @@ import loguru from cpg_flow import targets from cpg_flow import utils as cpg_flow_utils -from cpg_utils import Path, config, hail_batch +from cpg_utils import Path, config, hail_batch, to_path from cpg_seqr_loader import utils @@ -15,13 +15,15 @@ def create_combiner_jobs( multicohort: targets.MultiCohort, output_vds: Path, combiner_plan: Path, - temp_dir: Path, + temp_dir_string: str, job_attrs: dict[str, str], ) -> 'BashJob | None': vds_path: str | None = None sg_ids_in_vds: set[str] = set() sgs_to_remove: list[str] = [] + temp_dir = to_path(temp_dir_string) + # check for a VDS by ID - this is not the typical RD process if vds_id := config.config_retrieve(['workflow', 'use_specific_vds'], None): vds_result_or_none = utils.query_for_specific_vds(vds_id) diff --git a/src/cpg_seqr_loader/stages.py b/src/cpg_seqr_loader/stages.py index da9f9d1..e1fc789 100644 --- a/src/cpg_seqr_loader/stages.py +++ b/src/cpg_seqr_loader/stages.py @@ -35,7 +35,7 @@ class CombineGvcfsIntoVds(stage.MultiCohortStage): def expected_outputs(self, multicohort: targets.MultiCohort) -> dict[str, Path | str]: return { 'vds': self.prefix / f'{multicohort.name}.vds', - 'tmp': self.tmp_prefix / 'temp_dir', + 'tmp': str(self.tmp_prefix / 'temp_dir'), } def queue_jobs(self, multicohort: targets.MultiCohort, inputs: stage.StageInput) -> stage.StageOutput: @@ -45,7 +45,7 @@ def queue_jobs(self, multicohort: targets.MultiCohort, inputs: stage.StageInput) multicohort=multicohort, output_vds=outputs['vds'], combiner_plan=self.tmp_prefix / 'combiner_plan.json', - temp_dir=outputs['tmp'], + temp_dir_string=outputs['tmp'], job_attrs=self.get_job_attrs(multicohort), ) return self.make_outputs(multicohort, data=outputs, jobs=job)