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Recent Releases of cg

cg - Release v75.2.2

Fix(Sample Serialisation) Remove reference to flow_cells (#4590)

Fixed

  • Removes reference to unused property flow_cells

- Python
Published by clingen-sthlm 10 months ago

cg - Release v75.2.1

Patch subprocess check (#4585) (patch)

Fixed

  • The SubprocessSubmitter runs analyses with check False

- Python
Published by clingen-sthlm 10 months ago

cg - Release v75.2.0

Update Taxprofiler automation to use the AnalysisStarter (#4576) (minor)

Changed

  • Taxprofiler analyses are started with the AnalysisStarter

- Python
Published by clingen-sthlm 10 months ago

cg - Release v75.1.0

Integration test for mip-dna start-available (#4543)(minor)

Added

  • Integration test that runs the cg command workflow mip-dna start-available with one case ready to start. Checks that:

    • all necessary cli commands and http requests are made
    • all files are created in the correct place

  • Additional pytest plugin added: pytest-httpserver runs a barebones http server that captures calls made by the code under test.

  • Added default pytest option -m not integration so that integration tests are only run when the -m integration flag is added.

  • Run the integration tests in the GitHub action tests-coverage

- Python
Published by clingen-sthlm 10 months ago

cg - Release v75.0.10

Nallo add QC checks for peddy kinship and somalier sex (#4426)

Added

  • Nallo QC Peddy kinship
  • Nallo QC Somalier sex check

- Python
Published by clingen-sthlm 10 months ago

cg - Release v75.0.9

Feat(Vulture) Add Vulture pre-commit to cleanup dead code (#4430) (patch)

Description

Vulture is a popular tool for removing unused code in python. It was suggested in a meeting that it could be called automatically to help prune the codebase when refactoring modules.

Added

  • vulture to the pre-commit hooks
  • vulture_whitelist.txt for ignoring false positives

Changed

  • Removed almost all methods flagged by vulture

- Python
Published by clingen-sthlm 10 months ago

cg - Release v75.0.8

Remove APIRequest outside of TB (#4502) (patch)

Fixed

  • Removed APIRequest coupling outside of the TrailblazerAPI.

- Python
Published by clingen-sthlm 11 months ago

cg - Release v75.0.7

add check for fluffy sample sheet samples to belong to case (#4555)(patch)

Description

Closes #4554

Added

  • Check that the samples included in the Illumina sample sheet belong to the given Fluffy case and filter out the ones that don't

- Python
Published by clingen-sthlm 11 months ago

cg - Release v75.0.6

Rework subprocess submitter (#4549)(patch)

Description

Closes https://github.com/Clinical-Genomics/pipeline-integration/issues/56

In the pipeline integration flow, this PR creates the start command for non-Nextflow pipelines in a CaseConfig model method, instead of fetching it from formatting a dictionary in the Submitter.

Added

  • get_start_command method in MicrosaltCaseConfig
  • Test for the new method

Changed

  • Remove WORKFLOW_LAUNCH_COMMAND_MAP.

Co-authored-by: Rasmus Burge 80392398+RasmusBurge-CG@users.noreply.github.com Co-authored-by: Sebastian Diaz juan.sebastian.diaz.boada@scilifelab.se

- Python
Published by clingen-sthlm 11 months ago

cg - Release v75.0.5

DEV - Start Taxprofiler analyses using pipeline integration flow (#4509)(patch)

Description

Development branch for integrating Taxprofiler to the new AnalysisStarter flow To be merged with https://github.com/Clinical-Genomics/servers/pull/1676

Added

  • Class TaxprofilerParamsFileCreator
  • Base model TaxprofilerParameters inheriting from WorkflowParameters (empty as no extra parameters are needed)
  • Taxprofiler to configurator factory and to analysis starter factory
  • Dev cli commands:
    • devconfigcase
    • dev_run
    • dev_start
    • devstartavailable
  • Tests for new cli commands

Changed

  • Move the constructor from the child classes to the parent ParamsFileCreator. This constructor receives only the servers params file path. Override only in raredisease as it needs store and LIMS

Fixed

  • Enhance tests and fixtures of analysis start workflow

Co-authored-by: Linnéa Löfdahl linnea.lofdahl@scilifelab.se

- Python
Published by clingen-sthlm 12 months ago

cg - Release v75.0.4

Fix(dragen demux) Read bashrc to source the correct path

Description

With the latest dragen version (4.4.4) which is running on cg-dragen2. The dragen installation does not add the dragen binary to the bath.

I changed the bashrc for hiseq.clinical to export it but Slurm does not load the bashrc per default. This PR adds a flag to make it source it

Added

  • Added the -l flag to the Sbatch header to run it as a login-session and thereby loading the bashrc

- Python
Published by clingen-sthlm 12 months ago

cg - Release v75.0.3

Fix(microSALT) Don't delete Slurm file (#4529)(patch)

Description

See #4527 for issue description.

This PR removes the method which was mean to purge a file from previous runs, but instead removed the file that was relevant for the run just starting

Changed

  • Remove the method removing the microSALT Slurm IDs file

- Python
Published by clingen-sthlm 12 months ago

cg - Release v75.0.2

add support for starting microsalt case without all samples sequenced (#4520)(patch)

Description

Closes #4519

Added

  • Function that checks if sample is microSALT or Mutant to skip it if it has no reads and do not block the analysis
  • tests for new functionality

- Python
Published by clingen-sthlm 12 months ago

cg - Release v75.0.0

Replace RNAFUSION start, run and case config dev commands (#4503)(major)

Description

Closes https://github.com/Clinical-Genomics/pipeline-integration/issues/2

Rename the RNAFUSION dev commands (config-case, run, start and start-available) to replace production CLI commands.

Changed

  • Removes revision as a CLI option for RNAFUSION and raredisease
  • Removes stub_run from the analysis starting flow

Fixed

  • Remove tests for deprecated commands and unused RNAFUSION fixtures

- Python
Published by clingen-sthlm 12 months ago

cg - Release v74.1.3

Refactor sample sheet entry creation (#4510)(patch)

Description

Closes https://github.com/Clinical-Genomics/pipeline-integration/issues/19 Refactors the Nextflow sample sheet creation in the pipeline integration flow so that it does not need any Pydantic base model for its creation.

Added

  • Taxprofiler sample sheet creator

Changed

  • Validation for existence of fastqfiles relies exclusively on the input fetcher, not in the sample sheet
  • The return type of _get_paired_read_paths changed to a tuple iterator

- Python
Published by clingen-sthlm 12 months ago

cg - Release v74.1.2

clean raredisease analysis tests (#4501)(patch)

Description

Remove the analysis starter test dependencies on common fixtures.

Changed

  • remove io handler usages
  • remove writable file from fixtures

Fixed

  • Remove usages of io handler

- Python
Published by clingen-sthlm 12 months ago

cg - Release v74.1.1

add dev commands for raredisease (#4500)(patch)

Description

Add dev commands for raredisease analysis.

Added

  • devconfigcase
  • dev_run
  • dev_start
  • devstartavailable
  • Tests for these and rnafusion commands

Changed

  • Remove special exception of AnalysisRunningError in AnalysisStarter start_available
  • Parametrised AnalysisStarter tests on workflow (second parameterisation)

- Python
Published by clingen-sthlm 12 months ago

cg - Release v74.1.0

Add RNAFusion to Pipeline Implementation (#4483)(minor)

Added

  • dev-run CLI command
  • dev-start CLI command
  • dev-start-available CLI command
  • dev-config-case CLI command
  • RNAFusionSampleSheetCreator

  • RNAFusionParamsFileCreator

Changed

  • Refactored the SampleSheetCreator parent class to have more functionality

Co-authored-by: Isak Ohlsson Ångnell 40887124+islean@users.noreply.github.com Co-authored-by: Sebastian Diaz juan.sebastian.diaz.boada@scilifelab.se

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v74.0.0

replace microsalt cli commands (#4499)(major)

Description

Replace the production microsalt CLI commands with the dev commands from the pipeline integration project

Added

  • Tests for microsaltstart and start-available CLI commands

Changed

  • Use only @click.pass_obj instead of @click.pass_context in new CLI commands
  • Remove old CLI commands
  • Removed tests and fixtures for previous CLI commands Co-authored-by: Isak Ohlsson Ångnell 40887124+islean@users.noreply.github.com

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v73.2.0

Feat(Pacbio) Only run post-processing if all cells are ready (#4479)(minor)

Description

This PR changes the starting logic for the post-procesessing of Pacbio SMRT cells. Before post-processing each SMRT cell we now also check that all other cells in the same run directory also are completed.

This is only applies to the post_process_all_runs command. One can still run post_process_run to post-process a SMRT cell regardless of the others in the run

Changed

  • The post_process_all_runs now only post-pocesses SMRT cells if the entire run is completed

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v73.1.1

Feat(Scout) Add MIP-DNA to upload (#4425)

Added

  • tiddit_coverage_wig, upd_regions_bed and upd_sites_bed under sample in the Scout load config so the corresponding files are uploaded to Scout.

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v73.1.0

add Nallo loqusdb to cg upload (#4471) (minor)

Added

  • Nallo loqusdb to cg upload

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v73.0.5

Fix microSALT single sample tracking (#4496) (patch)

Fixed

  • Single sample cases gets a slurm job id file name with the whole sample id.

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v73.0.4

Exclude VCF-str file for WES Raredisease cases (#4485) (patch)

Fixed

  • WES Raredisease cases are not expected to have a vcf-str file in the Scout upload

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v73.0.3

Update raredisease params creation (#4482)(patch)

Description

Closes #4362 Implement changes to the raredisease params file creation in master to the pipeline integration workflow. Co-authored-by: Isak Ohlsson Ångnell 40887124+islean@users.noreply.github.com

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v73.0.2

Remove case argument (#4481) (patch)

Fixed

  • Removed case_id CLI argument from cg workflow microsalt dev-start-available

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v73.0.1

add error handling to fastq clean (#4206)(patch)

Description

Closes #3817 Adds error handling to the CLI command cg compress clean fastq so that any exception raised when cleaning a single sample is caught and logged without affecting the cleaning of other samples. Additionally, adds a check that verifies that a sample is not part of a newer case before cleaning.

Added

  • Error handling

Changed

  • The way samples to clean are fetched, now we verify if they belong to a case that is not cleanable.

Co-authored-by: eliott eliottob6@gmail.com Co-authored-by: EliottBo 112384714+eliottBo@users.noreply.github.com

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v73.0.0

fix completed at before started at in analysis table (#4455)(major)

Description

Part of #4454

Summary of changes

  1. Makes the fetching of Housekeeper versions for each analysis (in upload and generation of delivery reports) dependent on the version entry id instead of the equality between analysis.completed_at date and version date.
  2. Makes the analysis completed_at date be datetime.now() when called through the cg workflow store command, and not dependent on the deliverables file timestamp.

Added

  • Main method to get versions in the HousekeeperAPI gets version entry id as parameter, not bundle name and date
  • Remove optional parameter analysis_completed_at from generate_delivery_report CLI command

Changed

  • Make the AnalysisAPI.create_housekeeper_bundle method return a tuple of Housekeeper bundle and version (instead of returning None)
  • Make several delivery report API methods receive for parameter an Analysis object instead of the analysis.completed_at date

Fixed

  • Cleans unused functions and tests

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v72.0.4

Widen workflow version column (#4470) (patch)

Fixed

  • Workflow version is allowed to be up to 64 characters
  • data_analysis is not nullable

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v72.0.3

Add nallo loqusdb upload (#4344)

Added

  • Nallo upload to loqusDB using cg

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v72.0.2

Fix(PDC) Always fetch latest file (#3857)

Description

Added

  • A flag "-ifnewer" to the retrieval command.

Changed

  • This flag will "The ifnewer option replaces an existing file with the latest backup version only if the backup version is newer than the existing file." More on this here: https://www.ibm.com/docs/en/spectrum-protect/8.1.11?topic=reference-ifnewer

Fixed

  • This will fix this issue: https://github.com/Clinical-Genomics/cg/issues/3843

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v72.0.1

Feat(statusDB view) Add isarchived filter applicationversion (#4469) (patch)

Description

Added

  • Added the ability to filte on application.isarchived in the applicationversion table

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v72.0.0

DEV - Start pipelines (#4227) (major)

Added

  • microSALT CLI commands dev-run, dev-start and dev-start-available
  • AnalysisStarter
  • AnalysisStarterFactory
  • ConfiguratorFactory
  • Configurator (Parent)
  • MicrosaltConfigurator (Child)
  • NextflowConfigurator (Child)
  • MicrosaltConfigFileCreator
  • RarediseaseConfigFileCreator
  • RarediseaseParamsFileCreator
  • ManagedVariantsFileCreator
  • GenePanelsFileCreator
  • PipelineExtension (Parent)
  • RarediseaseExtension (Child)
  • InputFetcher (Parent)
  • FastqFetcher (Child)
  • Submitter (Parent)
  • SubprocessSubmitter (Child)
  • SeqeraPlatformSubmitter (Child)
  • SeqeraPlatformClient
  • Tracker (Parent)
  • MicrosaltTracker (Child)
  • NextflowTracker (Child)
  • Tests

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v71.4.0

remove contamination check in raredisease (#4463)(minor)

Changed

  • remove contamination check

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v71.3.1

Fix(statusDB Apptags) Add is_archived filter (#4466)(patch)

Description

Added

  • Ability to filter on is_archived in the ApplicationView

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v71.3.0

added new analysis column to db (#4459)(minor)

Description

Part of #4454 , adds the version id column to the Analysis table in the databse

Added

  • Indexed column housekeeperversionid to the Analysis table

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v71.2.0

Fix(Start query) Harmonize cases to start query (#4443)(minor)

Description

This PR harmonises the logic for getting which cases should be analysed. I removes all the special logic for Balsamic and MIP-DNA and centralises the logic to the database layer.

Important changes:

  • microSALT is now explicitly treated as an exception, and is the only pipeline that will start automatically if allready analysed but new data is added.

  • The start-available command no longer performs the SeqeuencingQC check. Instead it just queries the case.aggregated_sequencing_qc column in the database. The command cg sequencing-qc runs the same logic on a timer, so the will be performed by this command instead.

Changed

  • Sequencing QC removed from start-available
  • Sequencing QC added as a query filter in start-available
  • Removed special is_case_ready_for_analysis from MIP-DNA and Balsamic
  • Removed the extra _is_case_to_be_analyzed check in read.py

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v71.1.6

fix-raredisease-delivery-report-percentage (#4458)

Changed

  • Raredisease Delivery report: mapping fraction to percentage

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v71.1.5

Speed up CaseSample view (#4457) (patch)

Fixed

  • Search for names or internal ids in the CaseSample form. Speeds up the form

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v71.1.4

Create ticket inbox before rsync job (#4446)(patch)

Added

  • createinbox job creates the directory using mkdir -p which will not fail should the directory already exist
  • rsync job depends on the above job using the sbatch parameter --dependency=afterok:<JOBID> and so will not run before it's completed.

Changed

If the optional header --exclude is not included there will no longer be an empty #SBATCH header

Fixed

This will mean that the directory already exists when rsync runs and hopefully there will not be any more race conditions when running those jobs.

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v71.1.3

fix nextflow store available (#4451)(patch)

patches 4450

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v71.1.2

fix nextflow store available (#4450)(patch)

Description

The CLI command store-available for nextflow pipelines exited before all cases were evaluating for storing. This PR makes sure that click.abort is invoked only after all cases have been assesed and at least one got an exception caught.

Added

  • sentinel variable that changes from True to False when an exception is caught for the store-available commands

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v71.1.1

Speed up some admin forms (#4449) (patch)

Fixed

  • Analysis, orders and cases all have speedier forms.

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v71.1.0

Add Raredisease orderform support (#4444)(minor)

Description

Closes #4359

Changed

  • Updated 1508 order form fixtures to version 35
  • Parametrise orderform tests

Co-authored-by: Isak Ohlsson Ångnell 40887124+islean@users.noreply.github.com

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v71.0.8

Add links to the admin views (#4442) (patch)

Added

  • Customer columns link to the Customer table
  • Illumina Flow cell links to the Illumina Sample Sequencing Metrics table
  • Pacbio SMRT Cell links to the Pacbio Sample Sequencing Metrics table
  • Sample links to Application
  • Pool links to application
  • Application links to ApplicationVersion

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v71.0.7

Patch case latest analysed ensuring dates are not None (#4445)

Description

The Case.latest_analysed sorts the completed_at dates of a case's analyses. This fails when dates are None. This PR filters out analyses that have completed_at equal to None.

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v71.0.6

patch to get the expected analysis given a case (#4439)

Description

Closes https://github.com/Clinical-Genomics/bug-reports/issues/36

Added

-

Changed

  • cases.analysis[0] ocurrences with the correct store methods to fetch the latest completed analysis
  • cases.analysis is now sorted by created_at which is never None.

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v71.0.5

Mirosalt-version-storage (#4436) (patch)

Added

  • microsalt-version to protected tags for MICROSALT workflow and organized alphabetically

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v71.0.4

patch wrong analysis set as complete in cases with multiple analyses (#4435)

Description

The AnalysisAPI method update_analysis_as_completed_statusdb used in the store methods picked up the analysis with the latest completed_at date to be stored. Still, by this point all of the analyses of the case had completed_at = None, making the function pick up the wrong analysis for updating. This PR changes the sorting to started_at instead.

Added

  • New CRUD function get_latest_started_analysis_for_case with tests

Changed

  • AnalysisAPI method update_analysis_as_completed_statusdb so that it uses the new function

Co-authored-by: Linnéa Löfdahl linnea.lofdahl@scilifelab.se

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v71.0.3

Change inheritance model of store (#4428)

Description

Closes https://github.com/Clinical-Genomics/Team-Trocadero/issues/12

Changed

  • Make the Delete, Create and Update handlers inherit from the ReadHandler instead of BaseHandler
  • Remove ReadHandler from Store constructor
  • Rename all Hanlder classes adding the Mixin suffix
  • Move session methods from Store class to BaseHandler
  • Remove the instantiation of the Handlers in the init of the Store
  • Removes the __init__ from all handlers, all of them will use the constructor of the parent class (BaseHandler)

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v71.0.2

fix delivery report creation with completed_at date (#4431)

Description

Fix a current bug in production in which the delivery report generation tries to get a HK bundle version with a wrong datetime

Fixed

  • The version would be fetched through completed_at instead of started_at of the Analysis object
  • The completed_at date of teh Analysis object will be the timestamp of the bundle generated by HermesAPI

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v71.0.1

Fix(Nallo) Link Nallo to tower clean command (#4424)

Description

Adds Nallo as a valid workflow for the cg clean tower-past-run-dirscommand.

Fixed

  • Nallo is now a valid option for `cg clean tower-past-run-dirs

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v71.0.0

Add manual marking for cases sent to top-up (#4399) (major)

Added

  • Add new value for case action: top-up, set this value on a case to mark it for top up

  • Analysis row in StatusDB created at the start of analysis instead of on completion

  • Link analysis in StatusDB with analysis in Trailblazer by adding the column trailblazer_id to the table in StatusDB

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v70.0.8

Fix index-sequences (#4416)

Description

The customers provided the indices in the wrong order. Also they only use 48 of the indices so a large part has been removed. AZ has provided the correct indices for the endpoint to return

Fixed

  • Order of indices is now correct

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v70.0.7

Fix Tomte uploads (#4414) (patch)

Fixed

  • Loading RNA outlier variants to Scout only happens if files exist

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v70.0.6

Update gene_panel.py (#4412)

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v70.0.5

Nallo allow revision flag upon resume (#4409)

Added

  • allow revision flag upon resuming tower runs

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v70.0.4

change suffix from sortedmd to sortmd (#4405)

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v70.0.3

Fix error (#4404) (patch)

Fixed

  • Wrap a GoogleAuthError in our endpoint

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v70.0.2

Create one case per sample for metagenome orders (#4398)(patch)

Changed

  • Refactor StoreMetagenomeOrderService to create cases for each sample and add case testing

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v70.0.1

create customer/internal map file and feed-in to raredisease (#4390)

Added

  • Create a csv file with the corresponding customer and internal sample ids upon raredisease config-case

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v70.0.0

remove clean hk command that was unused (#4395)(major)

Description

The CLI function corresponding to the command cg clean hk-bundle-files is not used in the automation nor by any member of Clinical Genomics. Therefore, we decided to remove it from the codebase.

Fixed

  • Remove function hk_bundle_files from cg/cli/clean.py
  • Remove all functions that were only used there
  • Remove all tests of removed functions

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.10.10

Fix bind in most recent alembic migration (#4396)

Changed

Fixed issue preventing creation of new alembic revisions

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.10.9

Change Taxprofiler Sequencing QC (#4397) (patch)

Changed

  • Taxprofiler Sequencing QC is that all samples should have reads.

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.10.8

Include prioritized status in ScoutLoadConfig (#4392) (patch)

Added

  • status: prioritized to the scout load config if the priority of the case is priority or express

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.10.7

Fix orderform error when empty fields (#4394)(patch)

Added

  • BeforeValidator in ExcelSample model to make sure that the empty value for require_qc_ok tumour are converted to Non before validation

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.10.6

Feat(micro Orderform) Allow version 2 of the form (#4360) (patch)

Description

Changes are needed to the microbial_sequencing excel ordeform. This PR updates the current version and replaces the fixture file with the new version

Changed

  • Current version of microbial_sequencing ordeform updated from 1 to 2

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.10.5

Add limit flag for mip and balsamic start-available (#4381) (patch)

Added

  • --limit flag for number of cases to start with the start-available command for mip and balsamic.

Changed

  • Changed mip_dna_context to actually contain cases ready to be analysed that could be picked up by the start-available command.

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.10.4

Update RML form to v20 (#4371) (patch)

Added

  • Endpoint /orders/index_sequences for fetching index sequences

Changed

  • RML and Fluffy orders need to use v20 of the order form

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.10.3

add if statement for nallo scout (#4387)

Changed

  • Nallo delivery report link to scout38

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.10.2

Add Revio prep and sequencing step information to the LIMS constants (#4382) (patch)

Added

  • Step and UDF names of the Revio prep to the LIMS constants
  • Step and UDF names of the Revio sequencing to the LIMS constants

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.10.1

Add Nallo validation rule (#4384) (patch)

Fixed

  • validateexistingsamplescompatiblewithordertype used in the Nallo validation

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.10.0

Add support for raredisease orders (#4363)(minor)

Description

Adds validation and storing support to Raredisease orders. Uses all existing validation from MIP-DNA plus an additional validation that checks that all samples in a case have app tags belonging to the same prep category.

Added

  • New case validation rule validate_samples_in_case_have_same_prep_category for Raredisease and MIP-DNA
  • Utils function to get prep categories for samples of a case
  • Error model for multiple samples in a case having same prep category
  • Models for the validation of raredisease orders inheriting from MIP:
    • Order (fixing type hints for cases)
    • Case (fixing type hints for sample and for methods
    • Sample
  • Allowed Raredisease delivery types
  • Validation rules
  • Entry for Raredisease to Storing registry

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.9.0

Support Nallo excel form and bump pacbio (#4374) (minor)

Added

  • Nallo order form fixture
  • Support for parsing Nallo order forms

Changed

  • Bumped Pacbio raw data version to v2

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.8.6

Nallo Scout upload remove assembly (#4380)

Changed

  • Nallo Scout do not upload assembly file

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.8.5

Make alembic revision 8e0b9e03054d idempotent (#4378) (patch)

Fixed

The alembic migration for revision 8e0b9e03054d would fail if downgraded and then upgraded again. This change removes that issue.

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.8.4

Update metrics in Nallo delivery report (#4377)

Changed

  • additional metrics in Nallo delivery report

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.8.3

Add rows for raredisease in ordertypeapplication table (#4375) (patch)

Added

  • Migration to create copies of all MIPDNA entries in the ordertypeapplication table with RAREDISEASE as ordertype instead

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.8.2

add new prep step info (#4372)(patch)

Description

Added

  • New LIMS step information for the Watchmaker prep

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.8.1

Add capture kit validation for fastq orders (#4366) (patch)

Added

  • Validation of the capture kit for fastq orders

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.8.0

Add rule for resetting capture kit (#4331) (minor)

Added

  • resetoptionalcapture_kits rule

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.7.2

Fix(CI) Update version of bump2version version used (#4369) (patch)

Description

bump2version-ci cannot deal with double quotes "like these" in commit messages. This was patched in https://github.com/Clinical-Genomics/bump2version-ci/pull/12.

However we seem to still be using the old version in our github action

Changed

  • Now uses Clinical-Genomics/bump2version-ci@2.0.3 instead of Clinical-Genomics/bump2version-ci@v3

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.7.1

Fix existing sample check (#4354) (patch)

Added

  • Rule for validating that existing samples are compatible with the order type
  • Support for filtering samples in collaboration on order type

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.7.0

Added

  • When creating tags for orders, check if there is at least one sample which application is external.
  • In that case add the tag external-data to the order.

- Python
Published by mogmi about 1 year ago

cg - Release v69.6.4

RAREDISEASE & nf-analysis: change logic for skip_germlinevariant calling in config-case (#4330)

Added

  • Error throwing when a parameter is defined both in the servers yaml and built from cg

Changed

  • change logic for skip_germlinevariant calling in config-case
  • the default capture kit will be defined from servers configs, not cg

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.6.3

fix set for d4 (#4368)

Added

  • fix tag set for d4 file

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.6.2

add Raredisease order type to database (#4365)(MINOR)

Description

Closes #4364

Added

  • Raredisease to the OrderType Strenum
  • Alembic migration to allow new ordertype in the order_type_application table

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.6.1

Add tumour to MIP-RNA (#4356) (patch)

Added

  • Tumour field on MIP-RNA samples

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.6.0

Add validations for Nallo orders (#4342)(minor)

Description

Added

  • Models and validation rules to make Nallo orderable in cg

- Connect Nallo with CaseStoring service

Co-authored-by: Sebastian Diaz juan.sebastian.diaz.boada@scilifelab.se

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.5.3

Remove raredisease adapter QC check (#4325)

Changed

  • remove raredisease adapter QC check

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.5.2

Update to Pydantic v2 syntax (#4324) (patch)

Fixed

  • model_config instead of class Config

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.5.1

fixed scout url for nallo (#4346)(patch)

Description

Fixed

  • The url of Scout38 was missing the .sys.
  • For Nallo cases with delivery type scout the old Scout url would have been shown. Now it always checks for the workflow to choose the url.

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.5.0

add nallo ordertype and alembic migration (#4347)(minor)

Description

Closes #4348

Added

  • Nallo as an ordertype
  • Alembic migration to update the ordertype_application table with Nallo as ordertype

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.4.6

remove dupliate (#4353)

Added

  • remove dupliate entry for nallo housekeeper filepath

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.4.5

Finish up nallo scout upload (#4335)

Added

  • add peddy to nallo scout upload
  • add hificnv_coverage to nallo scout upload
  • add maf coverage to nallo scout upload
  • add alignement to nallo scout upload
  • add assembly alignment to nallo scout upload

Changed

-

Fixed

  • Removed double definition of NALLOCASETAGS and NALLOSAMPLETAGS

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.4.4

(patch) Patch AnalysisAPI instantiation (#4352) (patch)

Fixed

  • Workflow instead of workflow

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.4.3

add delivery message support for nallo (#4332)(patch)

Description

Closes #4341 Blocked by #4329

Add support for delivery messages for delivery types raw_data-analysis, raw_data-analysis-scout and raw_data-scout

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.4.2

fix types for delivery report for Nallo (#4345)(patch)

Description

Fix the NalloUploadAPI with the correct data types for creating the delivery report and upload to scout

Added

  • Data delivery types containing raw-data to the allowed types for delivery report creation

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.4.1

add peddy files for housekeeper (#4338)

Added

  • peddy files to housekeeper
  • sv vcf outputs per caller

Changed

  • name of repeats vcf and bam

- Python
Published by clingen-sthlm about 1 year ago

cg - Release v69.4.0

Add data delivery support for Nallo (#4329)(minor)

Description

Add delivery types for Nallo file delivery Closes #4326

Added

  • delivery types RAW_DATA_ANALYSIS, RAW_DATA_ANALYSIS_SCOUTand RAW_DATA_SCOUT in DataDelivery strenum
  • {bam} to the RAW_DATA_ANALYSIS_SAMPLE_TAGS
  • support for the new delivery types in theDeliveryServiceFactory

Changed

  • Removed BamDeliveryTagsFetcher and make BAM delivery use SampleAndCaseDeliveryTagsFetcher

- Python
Published by clingen-sthlm about 1 year ago