Template update 5.6.0 [CW-6070]
This commit is contained in:
Neil Horner
parent
a74a34763e
commit
18bf1d5b19
@ -8,7 +8,7 @@ repos:
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always_run: true
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pass_filenames: false
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additional_dependencies:
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- epi2melabs==0.0.57
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- epi2melabs==0.0.58
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- repo: https://github.com/pycqa/flake8
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rev: 5.0.4
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hooks:
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13
CHANGELOG.md
13
CHANGELOG.md
@ -4,6 +4,19 @@ All notable changes to this project will be documented in this file.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [Unreleased]
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### Changed
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- Updated to wf-template v5.6.0, changing:
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- Reduce verbosity of debug logging from fastcat which can occasionally occlude errors found in FASTQ files during ingress.
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- Log banner art to say "EPI2ME" instead of "EPI2ME Labs" to match current branding. This has no effect on the workflow outputs.
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### Fixed
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- Updated to wf-template v5.6.0, fixing:
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- dacite.exceptions.WrongTypeError during report generation when barcode is null.
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- Sequence summary read length N50 incorrectly displayed minimum read length, it now correctly shows the N50.
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- Sequence summary component alignment and coverage plots failed to plot under some conditions.
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## [v1.7.0]
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### Changed
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- `split_bam` and `build_minimap_index_transcriptome` process memory allocation increased.
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@ -48,7 +48,7 @@ therefore Nextflow will need to be
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installed before attempting to run the workflow.
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The workflow can currently be run using either
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[Docker](https://www.docker.com/products/docker-desktop)
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[Docker](https://docs.docker.com/get-started/)
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or [Singularity](https://docs.sylabs.io/guides/3.0/user-guide/index.html)
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to provide isolation of the required software.
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Both methods are automated out-of-the-box provided
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@ -1,9 +1,69 @@
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"""Common model classes used across all workflows."""
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from dataclasses import asdict, dataclass, field
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from decimal import Decimal
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from enum import Enum
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import json
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from typing import Any, Dict, List
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from pathlib import Path
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from typing import Any, Dict, List, Optional
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from ..util import get_named_logger # noqa: ABS101
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logger = get_named_logger("Models")
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@dataclass
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class WorkflowBaseModel:
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"""Common things for stuff in the model."""
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def get(
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self,
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field_name: str,
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title: bool = True,
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**kwargs
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):
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"""Get reportable field tuple."""
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field_info = self.__dataclass_fields__.get(field_name)
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# provide an empty string default title to minimise drama
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field_title = field_info.metadata.get("title", "")
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value = self.get_reportable_value(field_name=field_name, **kwargs)
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if title:
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return (field_title, value)
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return value
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def get_reportable_value(
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self,
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field_name: str,
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*,
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decimal_places: int = None,
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default_value: str = "N/A") -> Optional[str]:
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"""Get the value of a value and make it reportable."""
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# Get the field info using the field name
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field_info = self.__dataclass_fields__.get(field_name)
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if field_info is None:
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raise AttributeError(
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f"{field_name!r} is not a field on {self.__class__.__name__}"
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)
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value = getattr(self, field_name)
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if value is None:
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return default_value
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if isinstance(value, (int, float)):
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if decimal_places:
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value = round(value, decimal_places)
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if value < 0.0001 or value > 99999999:
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value = f"{value:.2E}"
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else:
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if decimal_places:
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raise TypeError(
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"decimal_places is not a supported argument for a non-numeric.")
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unit = field_info.metadata.get('unit')
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if unit:
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return f"{value} {unit}"
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return str(value)
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class SampleType(str, Enum):
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@ -86,10 +146,6 @@ class Sample:
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metadata={
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"title": "Sample alias",
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"description": "The alias for the sample given by the user"})
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barcode: str = field(
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metadata={
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"title": "Sample barcode",
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"description": "The physical barcode assigned to the sample"})
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sample_type: SampleType = field(
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metadata={
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"title": "Sample type",
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@ -98,10 +154,15 @@ class Sample:
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metadata={
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"title": "Sample pass",
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"description": "If true the sample has passed workflow checks"})
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barcode: str | None = field(
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default=None,
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metadata={
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"title": "Sample barcode",
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"description": "The physical barcode assigned to the sample"})
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additional_identifiers: List[SampleIdentifier] = field(
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default_factory=list, metadata={
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"title": "Additional sample identifiers",
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"description": "Addition identifiers for the sample"})
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"description": "Additional identifiers for the sample"})
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sample_checks: list[CheckResult] = field(
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default_factory=list, metadata={
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"title": "Sample checks",
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@ -123,9 +184,9 @@ class Sample:
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def get_sample_identifier(self, sample_identifier):
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"""Get a sample identifier given the identifier name."""
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for indentifier in self.additional_identifiers:
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if indentifier.name == sample_identifier:
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return indentifier.value
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for identifier in self.additional_identifiers:
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if identifier.name == sample_identifier:
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return identifier.value
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raise KeyError("Sample identifier not found")
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def set_sample_identifier(self, name, value):
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@ -139,7 +200,42 @@ class Sample:
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def to_json(self, filename):
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"""Save class as JSON."""
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with open(filename, 'w') as f:
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json.dump(asdict(self), f, default=str, indent=2, cls=DecimalEncoder)
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json.dump(asdict(self), f, default=str, indent=2)
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def get_reportable_qc_status(self, max_criteria=4):
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"""Store global status of the sample and list of QC criteria to show.
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:params max_criteria: Maximum number of criteria to be reported.
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"""
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# Store global status: pass/ failed
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qc_global_status = {"status": self.sample_pass, "scope": "QC status"}
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qc_criteria = []
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if self.sample_pass:
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qc_criteria.append(
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{"status": self.sample_pass, "scope": "All acceptance criteria met"}
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)
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else:
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# Report failed criteria until a maximum value
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for qc in self.sample_checks:
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if not qc.check_pass: # append criteria if failed
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qc_criteria.append(
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{
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"status": qc.check_pass,
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"category": qc.friendly_check_category(),
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"scope": qc.friendly_check_name(),
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}
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)
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if len(qc_criteria) > max_criteria:
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# Replace all the failed criteria, with a sentence with the number
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# instead of listing all of them.
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# Set status to False as more than max_criteria are failed.
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qc_criteria = [
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{
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"status": False,
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"scope": f"{len(qc_criteria)} acceptance criteria",
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},
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]
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return qc_global_status, qc_criteria
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@dataclass
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@ -161,7 +257,7 @@ class RunStats:
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@dataclass
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class WorkflowResult():
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class WorkflowResult(WorkflowBaseModel):
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"""
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Definition for results that will be returned by this workflow.
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@ -189,18 +285,73 @@ class WorkflowResult():
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default_factory=dict, metadata={
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"title": "Client fields",
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"description": "Arbitrary key-value pairs provided by the client"})
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versions: dict[str, Any] | None = field(
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default_factory=dict, metadata={
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"title": "Analysis tool versions",
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"description": """Key-value pairs collecting the
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software used and the corresponding versions"""})
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params: dict[str, Any] | None = field(
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default_factory=dict, metadata={
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"title": "Pertinent parameters",
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"description": """Key-value pairs with the
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options chosen by the user"""})
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def load_client_fields(self, filename):
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"""Load client fields."""
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with open(filename) as f:
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try:
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client_fields = json.loads(f.read())
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# convert any lists into strings for display
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for key, value in client_fields.items():
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if isinstance(value, list):
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client_fields[key] = ', '.join(value)
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except json.decoder.JSONDecodeError:
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client_fields = {"error": "Error parsing client fields file."}
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self.client_fields = client_fields
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return self.client_fields
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def load_params(self, params_json, keep=None):
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"""Create a workflow params dict."""
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params_json = Path(params_json)
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if keep is None:
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keep = []
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if not params_json.is_file():
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raise FileNotFoundError(f"No such file: {params_json}")
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with open(params_json, "r") as f:
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try:
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params_dict = json.loads(f.read())
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self.params = {
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k: v for k, v in params_dict.items() if k in set(keep)
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}
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return self.params
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except ValueError:
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raise ValueError(f"Invalid JSON file: {params_json}")
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def load_versions(self, versions_path):
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"""Create a version list of dict."""
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versions_path = Path(versions_path)
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if not versions_path.exists():
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raise FileNotFoundError(f"No such file: {versions_path}")
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if versions_path.is_dir():
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version_files = [
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vp for vp in versions_path.iterdir() if vp.is_file()
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]
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elif versions_path.is_file():
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version_files = [versions_path]
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else:
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raise IOError(f"{versions_path} should be either a directory or a file")
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for fname in version_files:
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versions = {}
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with open(fname, "r", encoding="utf-8") as fh:
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for line in fh.readlines():
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name, version = line.strip().split(",")
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versions[name] = version
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self.versions = versions
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return self.versions
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def to_json(self, filename):
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"""Save class as JSON."""
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with open(filename, 'w') as f:
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json.dump(asdict(self), f, default=str, indent=2, cls=DecimalEncoder)
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class DecimalEncoder(json.JSONEncoder):
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"""This should probably be moved."""
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def default(self, obj):
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"""Override the default method to handle Decimal objects."""
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if isinstance(obj, Decimal):
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return float(obj)
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return super().default(obj)
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json.dump(asdict(self), f, default=str, indent=2)
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@ -9,7 +9,7 @@ therefore Nextflow will need to be
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installed before attempting to run the workflow.
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The workflow can currently be run using either
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[Docker](https://www.docker.com/products/docker-desktop)
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[Docker](https://docs.docker.com/get-started/)
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or [Singularity](https://docs.sylabs.io/guides/3.0/user-guide/index.html)
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to provide isolation of the required software.
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Both methods are automated out-of-the-box provided
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@ -326,14 +326,16 @@ class NfcoreTemplate {
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String workflow_version = version(workflow)
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String.format(
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"""
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${colors.igreen}|||||||||| ${colors.reset}${colors.dim}_____ ____ ___ ____ __ __ _____ _ _
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${colors.igreen}|||||||||| ${colors.reset}${colors.dim}| ____| _ \\_ _|___ \\| \\/ | ____| | | __ _| |__ ___
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${colors.yellow}||||| ${colors.reset}${colors.dim}| _| | |_) | | __) | |\\/| | _| _____| |/ _` | '_ \\/ __|
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${colors.yellow}||||| ${colors.reset}${colors.dim}| |___| __/| | / __/| | | | |__|_____| | (_| | |_) \\__ \\
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${colors.iblue}|||||||||| ${colors.reset}${colors.dim}|_____|_| |___|_____|_| |_|_____| |_|\\__,_|_.__/|___/
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${colors.igreen}|||||||||| ${colors.reset}${colors.dim}_____ ____ ___ ____ __ __ _____
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${colors.igreen}|||||||||| ${colors.reset}${colors.dim}| ____| _ \\_ _|___ \\| \\/ | ____|
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${colors.yellow}||||| ${colors.reset}${colors.dim}| _| | |_) | | __) | |\\/| | _|
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${colors.yellow}||||| ${colors.reset}${colors.dim}| |___| __/| | / __/| | | | |__
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${colors.iblue}|||||||||| ${colors.reset}${colors.dim}|_____|_| |___|_____|_| |_|_____|
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${colors.iblue}|||||||||| ${colors.reset}${colors.bold}${workflow_name} ${workflow_version}${colors.reset}
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${NfcoreTemplate.dashedLine(monochrome_logs)}
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""".stripIndent()
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)
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}
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}
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@ -48,13 +48,6 @@ class Pinguscript {
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String paramsJSON = new JsonBuilder(params).toPrettyString()
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def params_data = new JsonSlurper().parseText(paramsJSON)
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// hostname
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def host = null
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try {
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host = InetAddress.getLocalHost().getHostName()
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}
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catch(Exception e) {}
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// OS
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// TODO check version on WSL
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def opsys = System.properties['os.name'].toLowerCase()
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@ -103,7 +96,7 @@ class Pinguscript {
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body_json \
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"tracking_id": [
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"msg_id": UUID.randomUUID().toString(),
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"version": "3.0.0"
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"version": "3.0.1"
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],
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"source": "workflow",
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"event": event,
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@ -123,7 +116,6 @@ class Pinguscript {
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],
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"env": [
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"user": user, // placeholder for any future okta
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"hostname": host,
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"os": [
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"name": opsys,
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"version": opver
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@ -96,7 +96,7 @@ params {
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]
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agent = null
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container_sha = "shac733d952a14257cf3c5c5d5d44c6aed84d5fe5a1"
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common_sha = "sha9ef2f4e4585c4ce6a604616e77185077551abf50"
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common_sha = "sha1c69fd30053aad5d516e9567b3944384325a0fee"
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}
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}
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@ -323,7 +323,12 @@
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"disable_ping": {
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"type": "boolean",
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"default": false,
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"description": "Enable to prevent sending a workflow ping."
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"description": "Enable to prevent sending a workflow ping.",
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"overrides": {
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"epi2mecloud": {
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"hidden": true
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}
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}
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},
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"version": {
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"type": "boolean",
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