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Recent Releases of https://github.com/clinical-genomics/hermes

https://github.com/clinical-genomics/hermes - Release 6.0.7

Merge pull request #139 from Clinical-Genomics/4275-add-bigbed-tag-to-upd-files (patch)

Added

  • bigbed tag to mip-dna upd files.

- Python
Published by clingen-sthlm 10 months ago

https://github.com/clinical-genomics/hermes - Release 6.0.6

Merge pull request #141 from Clinical-Genomics/mirosalt-version-storage

Added

  • microsalt-version tag to MicrosaltTags and update common tags

- Python
Published by clingen-sthlm 10 months ago

https://github.com/clinical-genomics/hermes - Release 6.0.5

adding wcx2cytosure (#138)

  • adding wcx2cytosure
  • use tag constants with fluffy

- Python
Published by clingen-sthlm 10 months ago

https://github.com/clinical-genomics/hermes - Release 6.0.4

Merge pull request #137 from Clinical-Genomics/updatenallotagssvscallers

Added

  • add new tags for per caller svs vcf #137 and peddy tags

- Python
Published by clingen-sthlm 11 months ago

https://github.com/clinical-genomics/hermes - Release 6.0.3

Merge pull request #136 from Clinical-Genomics/update_rd

Changed

  • no mitochondria in exome cases -> set as optional
  • remove multiqc detailed files, leaving just json and html
  • update nallo and raredisease docs

- Python
Published by clingen-sthlm about 1 year ago

https://github.com/clinical-genomics/hermes - Release 6.0.2

Merge pull request #134 from Clinical-Genomics/update_nallo

Added

-

Changed

  • update nallo tags to mimic raredisease for scout upload and fix paths

Fixed

-

- Python
Published by clingen-sthlm about 1 year ago

https://github.com/clinical-genomics/hermes - Release 6.0.1

Merge pull request #132 from Clinical-Genomics/add_nallo

Add nallo

- Python
Published by clingen-sthlm about 1 year ago

https://github.com/clinical-genomics/hermes - Release 6.0.0

feat(balsamic-qc): Remove (#128)(major)

Remove BalsamicQC

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

- Python
Published by clingen-sthlm about 1 year ago

https://github.com/clinical-genomics/hermes - Release 5.1.4

Balsamic v16.0.1 fix (#133)

Removed

  • case_report.html from balsamic delivery

- Python
Published by clingen-sthlm about 1 year ago

https://github.com/clinical-genomics/hermes - Release 5.1.3

feat(lint): Update

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/hermes - Release 5.1.2

Merge pull request #127 from Clinical-Genomics/add-dockerfile

Changed

  • Add dockerfile
  • Add dockerfile build actions -Add PR and Deployment instructions

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/hermes - Release 5.1.1

Update files and tags for balsamic release 16.0.0 (#117)

add balsamic release 16.0.0 files

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/hermes - Release 5.1.0

Update software versions file (#111)(minor)

Fixed

  • Correct name for software_versions.yml

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/hermes - Release 5.0.2

Merge pull request #126 from Clinical-Genomics/require-newer-pydantic (patch)

Fixed

  • Pydantic v2 is enforced in the toml

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/hermes - Release 5.0.1

Merge pull request #125 from Clinical-Genomics/update-pydantic-model

Changed

  • Update Pydantic models

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/hermes - Release 5.0.0

Merge pull request #124 from Clinical-Genomics/updste-python (major)

Changed

  • Update Python version to 3.12
  • Remove pkg_resource -Update deps

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/hermes - Release 4.4.13

Merge pull request #123 from Clinical-Genomics/update-eklipse

eKLIpse files removed from clinical-delivery but added to long-term-storage for observation

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/hermes - Release 4.4.12

Merge pull request #122 from Clinical-Genomics/add_manifest

Added

Add tags for manifest files in for nextflow pipelines Update docs with export for nextflow pipelines

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/hermes - Release 4.4.11

Merge pull request #120 from Clinical-Genomics/update-jinja2

Changed

  • Update Jinja2

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/hermes - Release 4.4.10

Merge pull request #121 from Clinical-Genomics/update-linters

Changed

  • Update linters

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/hermes - Release 4.4.9

Merge pull request #119 from Clinical-Genomics/update-setuptools

Changed

  • Update setuptools

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/hermes - Release 4.4.8

Merge pull request #118 from Clinical-Genomics/add-d4

add d4 files

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/hermes - Release 4.4.7

Add clinical-delivery and long-term-storage tags to Rnafusion (#115)

Added:

  • Add clinical-delivery and long-term-storage tags for Rnafusion

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/hermes - Release 4.4.6

Update rnafusion deliverable files to use sample ID instead of case ID (#104)(patch)

Changed

  • Use sample ID instead of case ID for rnafusion

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/hermes - Release 4.4.5

Merge pull request #114 from Clinical-Genomics/update_rd

Added

Add deliverable tag to qc-metrics deliver in raredisease to mimic Balsamic and MIP

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/hermes - Release 4.4.4

Merge pull request #109 from Clinical-Genomics/raredisease_store

Add raredisease HK tags

- Python
Published by clingen-sthlm almost 2 years ago

https://github.com/clinical-genomics/hermes - Release 4.4.3

Force storage of incomplete analyses (#113)

Added:

  • Force storage of incomplete analyses

- Python
Published by clingen-sthlm almost 2 years ago

https://github.com/clinical-genomics/hermes - Release 4.4.2

store params for tomte (#112) (patch)

Added

  • Adds the nextflow params file to store in HK for tomte

- Python
Published by clingen-sthlm almost 2 years ago

https://github.com/clinical-genomics/hermes - Release 4.4.1

Update tomte deliverables (#110) (patch)

Changed

  • Updated Tomte deliverables for upcoming version

- Python
Published by clingen-sthlm almost 2 years ago

https://github.com/clinical-genomics/hermes - Release 4.4.0

(feat taxprofiler): Store multiqc intermediate json files (#107)(minor)

Added

  • MultiQC intermediate files to HK

- Python
Published by clingen-sthlm almost 2 years ago

https://github.com/clinical-genomics/hermes - Release 4.3.0

Make tags as usable constants (#103) (minor)

Changed:

  • Converted tag dictionaries into StrEnum classes.

- Python
Published by clingen-sthlm almost 2 years ago

https://github.com/clinical-genomics/hermes - Release 4.2.2

Add tomte HK tags (#105) (patch)

Added

  • HK tags for tomte

- Python
Published by clingen-sthlm almost 2 years ago

https://github.com/clinical-genomics/hermes - Release 4.2.1

Store multiqc intermediate files for rnafusion (#101) (patch)

Added

  • MultiQC intermediate files for rnafusion

- Python
Published by clingen-sthlm about 2 years ago

https://github.com/clinical-genomics/hermes - Release 4.2.0

Add CONTRIBUTING and define tags for long-term storage and clinical delivery (#100) (minor)

Added:

  • Contributing document
  • long-term-storage tag
  • clinical-delivery tag

Changed:

  • Taxprofiler tags according to the new contribution guidelines

- Python
Published by clingen-sthlm about 2 years ago

https://github.com/clinical-genomics/hermes - Release 4.1.0

Merge pull request #99 from Clinical-Genomics/add_taxprofiler(minor)

Added

  • Add taxprofiler

- Python
Published by clingen-sthlm about 2 years ago

https://github.com/clinical-genomics/hermes - Release 4.0.2

Store intermediate MultiQC files for Balsamic (#95)

Added:

  • MultiQC intermediate files to HK
  • Added extra deliverable tag to metrics_deliverables.yaml

Changed:

  • Updated tags documents

- Python
Published by clingen-sthlm about 2 years ago

https://github.com/clinical-genomics/hermes - Release 4.0.1

Merge pull request #97 from Clinical-Genomics/add-codeowners

add(codeowners for autoamtic pr tracking)

- Python
Published by clingen-sthlm about 2 years ago

https://github.com/clinical-genomics/hermes - Release 4.0.0

Merge pull request #94 from Clinical-Genomics/refactor-pipeline-to-workflow (major)

Changes

  • Refactor pipeline to workflow

- Python
Published by clingen-sthlm about 2 years ago

https://github.com/clinical-genomics/hermes - Release 3.0.1

Remove Vogue tag, add Janus (#96)

Added

  • janus as a valid tag for the used_by field

Removed

  • vogue tag

- Python
Published by clingen-sthlm about 2 years ago

https://github.com/clinical-genomics/hermes - Release 3.0.0

Merge pull request #93 from Clinical-Genomics/refactor-pipeline-to-workflow-cgdeliverabels (major)

Changed

  • Refactor pipeline to workflow in CGDeliverables

- Python
Published by clingen-sthlm about 2 years ago

https://github.com/clinical-genomics/hermes - Release 2.0.0

Merge pull request #92 from Clinical-Genomics/rename-sars-cov-2-to-mutant (major)

Changed

  • Rename Sars-cov-2 to mutant

- Python
Published by clingen-sthlm about 2 years ago

https://github.com/clinical-genomics/hermes - Release 1.14.7

Add Gens files for Balsamic WGS analysis & update tags (#86)

Added:

  • Gens tags

Changed:

  • Cancer tags

- Python
Published by clingen-sthlm about 2 years ago

https://github.com/clinical-genomics/hermes - Release 1.14.6

Merge pull request #91 from Clinical-Genomics/rm-cgmodels

Change

  • Remove cgmodels
  • Rename Pipeline class to workflow to better describe the data

- Python
Published by clingen-sthlm about 2 years ago

https://github.com/clinical-genomics/hermes - Release 1.14.5

Merge pull request #90 from Clinical-Genomics/refactor-to-pep-0663

Changed

  • Refactor to PEP0663

- Python
Published by clingen-sthlm about 2 years ago

https://github.com/clinical-genomics/hermes - Release 1.14.4

Merge pull request #89 from Clinical-Genomics/refactor-to-pep-604

Change

  • Refactor to PEP 604

- Python
Published by clingen-sthlm about 2 years ago

https://github.com/clinical-genomics/hermes - Release 1.14.3

Merge pull request #88 from Clinical-Genomics/refactor-to-PEP-0585

Changed

  • Refactor to pep 0585

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/hermes - Release 1.14.2

Prepare deliverable files for rnafusion 3.0.1 (#85)

Added

  • Add gene expression
  • Add cram index
  • Add vcf

Changed

  • Fusion inspector and arriba-visualization output made as optional

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/hermes - Release 1.14.1

Merge pull request #87 from Clinical-Genomics/add-pre-commit

Added

  • Add pre commit and black action

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/hermes - Release 1.14.0

add nextclade ks-delivery tag (#84) (minor)

Added

ks-delivery tag to mutant nextclade output

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/hermes - Release 1.13.0

Add nextclade mutant (#82) (minor)

Added

  • nextclade summary for mutant delivery

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/hermes - Release 1.12.2

fix: PyYAML compatibility breakage after Cython v3.0 update (#83)

Fixes:

  • PyYAML compatibility breakage after Cython v3.0 update

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/hermes - Release 1.12.1

making fusion files optional for mip-rna (#81)

Changed

Makes files generated by MIP that related to fusions optional

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/hermes - Release 1.12.0

Python update (#79) (minor)

  • Updates to python 3.11 and typing-extensions 4.5

  • Updates github actions python version

  • Updates pytest to latest and adds typer 0.9

  • Adds noargsis_help=True to typer

Co-authored-by: Emil Bertilsson emil.bertilsson@hasta.scilifelab.se

- Python
Published by clingen-sthlm almost 3 years ago

https://github.com/clinical-genomics/hermes - Release 1.11.2

update: Store CNR and TMB files balsamic (#71)

- Python
Published by clingen-sthlm almost 3 years ago

https://github.com/clinical-genomics/hermes - Release 1.11.1

add metrics files for rnafusion (#77) (patch)

Added

  • metrics-qc and multiqc-json tags for rnafusion

- Python
Published by clingen-sthlm almost 3 years ago

https://github.com/clinical-genomics/hermes - Release 1.11.0

adds tags for mobile elements (#75)

Added

  • tags for mobile elements

- Python
Published by clingen-sthlm almost 3 years ago

https://github.com/clinical-genomics/hermes - Release 1.10.1

Update rnafusion tags (#76) (patch)

Changed

  • Updates rnafusion tags: adds cram and removes pizzly and squid

- Python
Published by clingen-sthlm almost 3 years ago

https://github.com/clinical-genomics/hermes - Release 1.10.0

Poetry update (#74) (minor)

  • Updates poetry lock file

  • Updates poetry version for actions

Co-authored-by: Emil Bertilsson emil.bertilsson@hasta.scilifelab.se

- Python
Published by clingen-sthlm almost 3 years ago

https://github.com/clinical-genomics/hermes - Release 1.9.0

Update rnafusion tags (#70) (minor)

Changed

  • Updated RNAfusion tags

- Python
Published by clingen-sthlm about 3 years ago

https://github.com/clinical-genomics/hermes - Release 1.8.0

Add RNAfusion (#62) (minor)

Added

  • RNAfusion tags

- Python
Published by clingen-sthlm over 3 years ago

https://github.com/clinical-genomics/hermes - Release 1.7.10

Balsamic v11 tags (#67)

Changed:

  • Balsamic tags

- Python
Published by clingen-sthlm over 3 years ago

https://github.com/clinical-genomics/hermes - Release 1.7.9

Merge pull request #69 from Clinical-Genomics/update_actions (patch)

Changed

  • Update GitHub actions

- Python
Published by clingen-sthlm over 3 years ago

https://github.com/clinical-genomics/hermes - Release 1.7.8

adding tags for reviewer (#64)

Added

  • Tags for reviewer

- Python
Published by clingen-sthlm over 3 years ago

https://github.com/clinical-genomics/hermes - Release 1.7.7

Merge pull request #68 from Clinical-Genomics/create_deployment (patch)

Added

  • Creates deployment instructions

- Python
Published by clingen-sthlm over 3 years ago

https://github.com/clinical-genomics/hermes - Release 1.7.6

Merge pull request #66 from Clinical-Genomics/Use-new-generic-update-script (patch)

Changed

  • Update deployments to use new generic update script
  • Update PR template

- Python
Published by clingen-sthlm over 3 years ago

https://github.com/clinical-genomics/hermes - Release 1.7.5

update poetry version (#65)

Fixed:

  • Update github actions poetry version to 1.2.0

- Python
Published by clingen-sthlm over 3 years ago

https://github.com/clinical-genomics/hermes - Release 1.7.4

Merge pull request #63 from Clinical-Genomics/deployment-instructions (patch)

Changed

Update deployment instructions on hasta

- Python
Published by clingen-sthlm over 3 years ago

https://github.com/clinical-genomics/hermes - Release 1.7.3

Make mutant reverse read tag optional (patch)

Changed

*Make mutant reverse read tag optional

- Python
Published by clingen-sthlm over 3 years ago

https://github.com/clinical-genomics/hermes - Release 1.7.2

Balsamic UMI & QC pipelines (#59)

Added

  • Balsamic UMI and QC pipeline specific implementations

- Python
Published by clingen-sthlm over 3 years ago

https://github.com/clinical-genomics/hermes - Release 1.7.1

Merge pull request #60 from Clinical-Genomics/mip-gens

Mip gens

- Python
Published by clingen-sthlm almost 4 years ago

https://github.com/clinical-genomics/hermes - Release 1.7.0

Update BALSAMIC tags (#56) (minor)

Added

  • Balsamic tumor-only WGS tests

Changed

  • Balsamic tags & structure of the config file

- Python
Published by clingen-sthlm almost 4 years ago

https://github.com/clinical-genomics/hermes - Release 1.6.16

adding qc-metrics tags (#37)

Added

- Python
Published by clingen-sthlm almost 4 years ago

https://github.com/clinical-genomics/hermes - Release 1.6.15

UMI cram fix (#55)

Fixed:

  • UMI cram files upload to scout.

- Python
Published by clingen-sthlm about 4 years ago

https://github.com/clinical-genomics/hermes - Release 1.6.14

add: balsamic UMI cram files/tags (#53)

Added

  • BALSAMIC UMI cram files to HK

- Python
Published by clingen-sthlm about 4 years ago

https://github.com/clinical-genomics/hermes - Release 1.6.13

remove: balsamic metrics tag (#54)

Removed

  • Balsamic QC metrics tag

- Python
Published by clingen-sthlm about 4 years ago

https://github.com/clinical-genomics/hermes - Release 1.6.12

makes stringtie output optional (#52)

Fixed

Made stringtie and gffcompare output optional

- Python
Published by clingen-sthlm about 4 years ago

https://github.com/clinical-genomics/hermes - Release 1.6.11

workaround: Balsamic producing same tags for delly & ascat filtered vcfs (#50)

- Python
Published by clingen-sthlm about 4 years ago

https://github.com/clinical-genomics/hermes - Release 1.6.10

Bump version: 1.6.8 → 1.6.9 [skip ci]

- Python
Published by clingen-sthlm about 4 years ago

https://github.com/clinical-genomics/hermes - Release 1.6.8

Update mutant deliverables (#47) (patch)

Added

  • Mutant tags for vogue and versions file

- Python
Published by clingen-sthlm over 4 years ago

https://github.com/clinical-genomics/hermes - Release 1.6.7

Updated Balsamics manta tag for WGS (#48)

- Python
Published by clingen-sthlm over 4 years ago

https://github.com/clinical-genomics/hermes - Release 1.6.6

fix: CHANGELOG version (#46)

- Python
Published by clingen-sthlm over 4 years ago

https://github.com/clinical-genomics/hermes - Release 1.6.5

changed tag: balsamics PNG plots to PDF file tag (#45)

- Python
Published by clingen-sthlm over 4 years ago

https://github.com/clinical-genomics/hermes - Release 1.6.4

feat: balsamic report tags (#42)

- Python
Published by clingen-sthlm over 4 years ago

https://github.com/clinical-genomics/hermes - Release 1.6.3

Update deployment instructions and move to readme #43 (patch)

Changed

  • Deploy instructions updated

- Python
Published by clingen-sthlm over 4 years ago

https://github.com/clinical-genomics/hermes - Release 1.6.2

Bump version: 1.6.0 → 1.6.1 [skip ci]

- Python
Published by clingen-sthlm over 4 years ago

https://github.com/clinical-genomics/hermes - Release 1.6.1

feat: BALSAMIC yaml QC metric tags (#39)

  • BALSAMIC metrics tags

- Python
Published by clingen-sthlm over 4 years ago

https://github.com/clinical-genomics/hermes - Release 1.6.0

Stop storing balsamic bam #38 (minor)

Changed

  • Stop storing balsamic bam in housekeeper

- Python
Published by clingen-sthlm over 4 years ago

https://github.com/clinical-genomics/hermes - Release 1.5.4

Merge pull request #32 from Clinical-Genomics/feat/storeumi20210714

BALSAMIC: store umi

- Python
Published by clingen-sthlm over 4 years ago

https://github.com/clinical-genomics/hermes - Release 1.5.3

Feature/mitodel (#36)

  • Add mitodel tags

  • Update deliverables file

  • Update list of tags

  • Update changelog

  • Fix version in changelog

  • Change is_mandatory tag from true to false

- Python
Published by clingen-sthlm over 4 years ago

https://github.com/clinical-genomics/hermes - Release 1.5.2

Feat update bumpversion CI (#34) (patch)

Changed

  • Use bump2version-ci@v3

- Python
Published by clingen-sthlm over 4 years ago

https://github.com/clinical-genomics/hermes - Release 1.5.1

Add bump2version-ci workflow

Added

  • bump2version-ci integration
  • Publish to PyPi on release

- Python
Published by clingen-sthlm over 4 years ago

https://github.com/clinical-genomics/hermes - 1.2.0

  • New deployment instructions using bumpversion and poetry

- Python
Published by henrikstranneheim almost 5 years ago

https://github.com/clinical-genomics/hermes - v1.0.0

- Python
Published by Mropat almost 5 years ago

https://github.com/clinical-genomics/hermes - v0.9.1

- Python
Published by Mropat almost 5 years ago

https://github.com/clinical-genomics/hermes - Balsamic update

- Python
Published by Mropat almost 5 years ago

https://github.com/clinical-genomics/hermes - Pipeline import

- Python
Published by Mropat about 5 years ago

https://github.com/clinical-genomics/hermes - Mutant support

This supports deliverables from the mutant pipeline

- Python
Published by moonso about 5 years ago