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Add Nallo clean-past-run-dirs #4289

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Add Nallo clean-past-run-dirs #4289

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2 changes: 2 additions & 0 deletions cg/cli/clean.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@
mip_dna_past_run_dirs,
mip_rna_past_run_dirs,
mutant_past_run_dirs,
nallo_past_run_dirs,
rnafusion_past_run_dirs,
rsync_past_run_dirs,
tower_past_run_dirs,
Expand Down Expand Up @@ -66,6 +67,7 @@ def clean():
mip_dna_past_run_dirs,
mip_rna_past_run_dirs,
mutant_past_run_dirs,
nallo_past_run_dirs,
rnafusion_past_run_dirs,
rsync_past_run_dirs,
microsalt_past_run_dirs,
Expand Down
2 changes: 2 additions & 0 deletions cg/cli/utils.py
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Expand Up @@ -4,6 +4,7 @@
import rich_click as click

from cg.constants import Workflow
from cg.meta.workflow.nallo import NalloAnalysisAPI
from cg.meta.workflow.raredisease import RarediseaseAnalysisAPI
from cg.meta.workflow.rnafusion import RnafusionAnalysisAPI
from cg.meta.workflow.taxprofiler import TaxprofilerAnalysisAPI
Expand All @@ -27,6 +28,7 @@ def is_case_name_allowed(name: str) -> bool:


TOWER_WORKFLOW_TO_ANALYSIS_API_MAP: dict = {
Workflow.NALLO: NalloAnalysisAPI,
Workflow.RAREDISEASE: RarediseaseAnalysisAPI,
Workflow.RNAFUSION: RnafusionAnalysisAPI,
Workflow.TAXPROFILER: TaxprofilerAnalysisAPI,
Expand Down
17 changes: 17 additions & 0 deletions cg/cli/workflow/commands.py
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Expand Up @@ -22,6 +22,7 @@
from cg.meta.workflow.mip_dna import MipDNAAnalysisAPI
from cg.meta.workflow.mip_rna import MipRNAAnalysisAPI
from cg.meta.workflow.mutant import MutantAnalysisAPI
from cg.meta.workflow.nallo import NalloAnalysisAPI
from cg.meta.workflow.nf_analysis import NfAnalysisAPI
from cg.meta.workflow.rnafusion import RnafusionAnalysisAPI
from cg.models.cg_config import CGConfig
Expand Down Expand Up @@ -337,6 +338,22 @@ def mutant_past_run_dirs(
)


@click.command("nallo-past-run-dirs")
@SKIP_CONFIRMATION
@DRY_RUN
@ARGUMENT_BEFORE_STR
@click.pass_context
def nallo_past_run_dirs(
context: click.Context, before_str: str, skip_confirmation: bool = False, dry_run: bool = False
):
"""Clean up of "old" Nallo case run dirs."""

context.obj.meta_apis["analysis_api"] = NalloAnalysisAPI(context.obj)
context.invoke(
past_run_dirs, skip_confirmation=skip_confirmation, dry_run=dry_run, before_str=before_str
)


@click.command("rnafusion-past-run-dirs")
@SKIP_CONFIRMATION
@DRY_RUN
Expand Down
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