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fix: bugfix of version crash when pipeline runs over several days #490

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merged 3 commits into from
Sep 25, 2024
Merged

fix: bugfix of version crash when pipeline runs over several days #490

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2407c7e
fix: bugfix of version crash when pipeline runs over several days
jonca79 Sep 24, 2024
b924f43
fix: update hydra min version
jonca79 Sep 24, 2024
48255ed
style: snakefmt
jonca79 Sep 24, 2024
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20 changes: 12 additions & 8 deletions workflow/rules/common.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ from hydra_genetics.utils.software_versions import touch_software_version_file
from hydra_genetics.utils.software_versions import use_container


hydra_min_version("1.14.0")
hydra_min_version("3.0.0")

min_version("7.13.0")

Expand Down Expand Up @@ -74,20 +74,24 @@ with open(config["output"]) as output:

validate(output_spec, schema="../schemas/output_files.schema.yaml")

date_string = datetime.now().strftime("%Y%m%d")
pipeline_version = get_pipeline_version(workflow, pipeline_name="Twist_Solid")
version_files = touch_pipeline_version_file_name(pipeline_version, date_string=date_string, directory="results/versions/software")
## get version information on pipeline, containers and software

pipeline_name = "Twist_Solid"
pipeline_version = get_pipeline_version(workflow, pipeline_name=pipeline_name)
version_files = touch_pipeline_version_file_name(
pipeline_version, date_string=pipeline_name, directory="results/versions/software"
)
if use_container(workflow):
version_files.append(touch_software_version_file(config, date_string=date_string, directory="results/versions/software"))
version_files.append(touch_software_version_file(config, date_string=pipeline_name, directory="results/versions/software"))
add_version_files_to_multiqc(config, version_files)


onstart:
export_pipeline_version_as_file(pipeline_version, date_string=date_string, directory="results/versions/software")
export_pipeline_version_as_file(pipeline_version, date_string=pipeline_name, directory="results/versions/software")
if use_container(workflow):
update_config, software_info = add_software_version_to_config(config, workflow, False)
export_software_version_as_file(software_info, date_string=date_string, directory="results/versions/software")
export_config_as_file(update_config, date_string=date_string, directory="results/versions")
export_software_version_as_file(software_info, date_string=pipeline_name, directory="results/versions/software")
export_config_as_file(update_config, date_string=pipeline_name, directory="results/versions")


### Set wildcard constraints
Expand Down
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