Repository navigation

Feature: co-assemblies submission with --mode metagenomic_assembly - #66

Draft

ochkalova wants to merge 33 commits into

devfrom

feat/coassembly_submission

Draft

Feature: co-assemblies submission with --mode metagenomic_assembly#66
ochkalova wants to merge 33 commits into
devfrom
feat/coassembly_submission

Commits on May 13, 2026
- explicitly set test_upload = true in test configs
  ochkalova
  committed
  7d1c0dd
- add partial co assembly support in ASSEMBLYSUBMIT
  
  ochkalova
  and
  Copilot
  committed
  100c7c0
Commits on May 14, 2026
- add REGISTER_COASSEMBLY_SAMPLE
  
  ochkalova
  and
  Copilot
  committed
  a65c94c
- minor refactoring of register_coassembly_sample.py
  
  ochkalova
  and
  Copilot
  committed
  b0689c6
- add default metadata values for register_coassembly_sample.py
  
  ochkalova
  and
  Copilot
  committed
  33f3967
- minor refactoring of register_coassembly_sample.py
  
  ochkalova
  and
  Copilot
  committed
  1f738cb
- disable publishDir for REGISTER_COASSEMBLY_SAMPLE
  ochkalova
  committed
  25d0171
Commits on Aug 5, 2026
- Merge branch 'dev' into feat/coassembly_submission
  ochkalova
  authored
  7e2c7aa
Commits on Aug 10, 2026
- update samplesheet header
  ochkalova
  committed
  29a6b8c
- append hash to co assembly sample if run in --test mode
  ochkalova
  committed
  afd7ae1
- add saveguard against duplicated accession in run_accession column
  ochkalova
  committed
  a9155e9
Commits on Oct 15, 2026
- add co assembly support for coverage calculation
  ochkalova
  committed
  a8e81a2
- add snapshot
  ochkalova
  committed
  9210a17
Commits on Oct 16, 2026
- add private data support for cooassembly sample registration
  ochkalova
  committed
  4461b2d
- revert test_upload changes in assembly test configs
  
  ochkalova
  and
  claude
  committed
  06c5ffc
- move samplesheets to test datasets folder
  ochkalova
  committed
  8eb09b5
- do not use hardcoded submission study in tests
  ochkalova
  committed
  f0cf4f2
- update tests and snapshots
  ochkalova
  committed
  d97e1ce
- update docs
  ochkalova
  committed
  4401ad2
Commits on Oct 19, 2026
- update REGISTER_COASSEMBLY_SAMPLE versions to topics
  ochkalova
  committed
  0c92b6d
- update BioSample regex
  ochkalova
  committed
  90bd671
Commits on Oct 20, 2026
- Merge branch 'dev' into feat/coassembly_submission
  ochkalova
  committed
  54b14fe
- make sure read files exist with checkIfExists: true
  ochkalova
  committed
  29fbe91
- add guard against empty files in calculateCoassemblyCoverage
  ochkalova
  committed
  0181af9
- update snapshot
  ochkalova
  committed
  3e72efa
Commits on Oct 29, 2026
- Address review comments in register_coassembly_sample.py
  
  ochkalova
  and
  claude
  committed
  0d6d64e
- Update CHANGELOG and co-assembly docs after review
  ochkalova
  committed
  3f4d424
- Merge branch 'dev' into feat/coassembly_submission
  ochkalova
  authored
  51daaba
- add more assertions for co assembly tests
  ochkalova
  committed
  07abba4
- update snapshots
  ochkalova
  committed
  38a69db
- keep only tax_id input arg instead of tax_id and scientific_name, because name is defined by the tax_id
  ochkalova
  committed
  ca52057
- add tax_id column for co assembly submssion
  ochkalova
  committed
  1851faa
- fix errorStrategy definition in GENERATE_ASSEMBLY_MANIFEST
  ochkalova
  committed
  9d2a06a

Commits

Commits on May 13, 2026

Commits on May 14, 2026

Commits on Aug 5, 2026

Commits on Aug 10, 2026

Commits on Oct 15, 2026

Commits on Oct 16, 2026

Commits on Oct 19, 2026

Commits on Oct 20, 2026

Commits on Oct 29, 2026