Repository navigation

Initial release - #72

Merged

KateSakharova merged 344 commits into

mainfrom

dev

Jul 31, 2026

Merged

Initial release#72
KateSakharova merged 344 commits into
mainfrom
dev

This pull request is big! We're only showing the most recent 250 commits

Commits on Mar 6, 2026
Commits on Mar 8, 2026
- fix: bugfixes revealed by testing
  ochkalova
  committed
  6e31241
- add more test cases for assemblysubmit
  ochkalova
  committed
  27b75b2
- to be fixed: create empty test.config to satisfy linter
  ochkalova
  committed
  38e68d6
Commits on Mar 9, 2026
- fix: update README for ENA submission examples
  ochkalova
  committed
  bd9a67f
- Merge pull request #26 from nf-core/assembly_workflow
  ochkalova
  authored
  da12288
Commits on Mar 10, 2026
- WIP
  KateSakharova
  committed
  c71b6f7
- Template update for nf-core/tools version 3.4.1
  KateSakharova
  committed
  b11c901
Commits on Mar 11, 2026
- RNA detection subwf
  KateSakharova
  committed
  e2843f4
- Merge pull request #23 from nf-core/feature/rna_detection
  KateSakharova
  authored
  f904453
- added checkm2 and coverm_genome
  KateSakharova
  committed
  7bad55e
- coverm works
  KateSakharova
  committed
  de1670d
- wip checkm2
  KateSakharova
  committed
  7282a43
- wip checkm2
  KateSakharova
  committed
  e8850d1
- checkm2 works
  KateSakharova
  committed
  7411db6
Commits on Mar 12, 2026
- minor issues
  KateSakharova
  committed
  157f9a5
- lint
  KateSakharova
  committed
  7b074e8
- minor README update
  ochkalova
  committed
  30b5fa4
- rewrite count_rna.py to correctly count rRNA genes and add test
  ochkalova
  committed
  3458596
- minor fixes
  KateSakharova
  committed
  5d8bcfb
- minor fixes
  KateSakharova
  committed
  5c8088c
- minor fixes
  KateSakharova
  committed
  10de6cd
- Merge pull request #34 from nf-core/feature/add-stats-genomesubmit
  KateSakharova
  authored
  d6a32c1
Commits on Mar 13, 2026
- remove license comments from count_rna.py
  ochkalova
  committed
  428ef6d
- Installed the fasta_classify_catpack subworkflow
  mberacochea
  committed
  03eef16
- Update documentation, add a new methods.md file detailing internal methods for RNA detection and assembly coverage
  ochkalova
  committed
  c77aab2
- revert docs/README.md to satisfy linter
  ochkalova
  committed
  560a920
- Merge pull request #37 from nf-core/bugfix/rna_count
  ochkalova
  authored
  966285b
- WIP implementing taxonomy
  KateSakharova
  committed
  1ffbcb7
Commits on Mar 16, 2026
- add taxa to meta
  KateSakharova
  committed
  00d0409
- some fixes after review
  KateSakharova
  committed
  3cd524a
- Merge pull request #38 from nf-core/feature/catpack-for-metagenomic-taxa-classification
  KateSakharova
  authored
  2b64c73
Commits on Mar 25, 2026
- Feature/studysubmit (#36)
  timrozday-mgnify
  authored
  8c3e48d
Commits on Mar 30, 2026
- Add tests, use ena-webin-cli handler, refactor modules.conf and update docs (#39)
  ochkalova
  authored
  4a8d78a
Commits on Apr 24, 2026
- add CREATE_ASSEMBLY_METADATA_CSV module, add versions tracking for all modules
  ochkalova
  committed
  8a37c4f
- add CREATE_GENOME_METADATA_TSV module
  ochkalova
  committed
  4bb213f
Commits on Apr 27, 2026
- refactor metadata files creating modules
  ochkalova
  committed
  6340b4b
Commits on Apr 28, 2026
- add find_concatenate module
  ochkalova
  committed
  7cb2880
- patch find/concatenate
  ochkalova
  committed
  c6b7fbc
- fix version statement for GENERATE_ASSEMBLY_MANIFEST module
  ochkalova
  committed
  8304fbf
- add FIND_CONCATENATE to assemblysubmit and update tests
  ochkalova
  committed
  f217ac8
- add FIND_CONCATENATE to genomesubmit and update tests
  ochkalova
  committed
  48abbfd
- Template update for nf-core/tools version 4.0.0
  nf-core-bot
  committed
  34728e8
- add additional inputs instead of params usage subwf
  ochkalova
  committed
  7aadf72
- add additional inputs instead of params usage in ENA_WEBIN_CLI_WRAPPER
  ochkalova
  committed
  26b3951
- add additional inputs in GENOME_UPLOAD
  ochkalova
  committed
  f6aaccc
- add additional inputs in GENERATE_ASSEMBLY_MANIFEST
  ochkalova
  committed
  b8b0d42
- update tests
  ochkalova
  committed
  9b02a4b
- fix checkm2_db definition
  ochkalova
  committed
  108ee4d
- remove --upload_force param because it's unnecessary for a user
  ochkalova
  committed
  70e5af3
- do not reference params in ASSEMBLYSUBMIT and GENOMESUBMIT
  ochkalova
  committed
  e296d89
- add test_upload parameter to REGISTERSTUDY and GENERATE_ASSEMBLY_MANIFEST processes
  ochkalova
  committed
  3910466
- rename checkm2_db_zenodo_id to checkm2_db_download_id for consistency
  ochkalova
  committed
  7bc9408
- add missing REGISTERSTUDY input
  ochkalova
  committed
  404c94b
- rename webincli_submit to webincli_mode
  ochkalova
  committed
  6a1152b
- add additional inputs instead of params usage subwf
  ochkalova
  committed
  badfb2b
- add additional inputs instead of params usage in ENA_WEBIN_CLI_WRAPPER
  ochkalova
  committed
  47b8698
- add additional inputs in GENOME_UPLOAD
  ochkalova
  committed
  c410d5e
- add additional inputs in GENERATE_ASSEMBLY_MANIFEST
  ochkalova
  committed
  708cb1e
- update tests
  ochkalova
  committed
  fd698fd
- fix checkm2_db definition
  ochkalova
  committed
  689259a
- remove --upload_force param because it's unnecessary for a user
  ochkalova
  committed
  74fa995
- do not reference params in ASSEMBLYSUBMIT and GENOMESUBMIT
  ochkalova
  committed
  1371dec
- add test_upload parameter to REGISTERSTUDY and GENERATE_ASSEMBLY_MANIFEST processes
  ochkalova
  committed
  93439b4
- rename checkm2_db_zenodo_id to checkm2_db_download_id for consistency
  ochkalova
  committed
  ff2d46d
- add missing REGISTERSTUDY input
  ochkalova
  committed
  7a6030c
- rename webincli_submit to webincli_mode
  ochkalova
  committed
  4cf9a0e
- add CREATE_ASSEMBLY_METADATA_CSV module, add versions tracking for all modules
  ochkalova
  committed
  4530c73
- add CREATE_GENOME_METADATA_TSV module
  ochkalova
  committed
  0b2d785
- add FIND_CONCATENATE to assemblysubmit and update tests
  ochkalova
  committed
  c7b2603
- update snapshot
  ochkalova
  committed
  5e435bf
- Merge branch 'dev' into feat/metadata_modules
  ochkalova
  authored
  555e4a1
- update snapshot
  ochkalova
  committed
  aafeff6
- add citations
  KateSakharova
  committed
  c2c7ba6
- test custom data in multiqc. So far it works with files _mqc prefix
  KateSakharova
  committed
  84b94b7
- add custom tables to multiqc
  KateSakharova
  committed
  e48194f
- wip
  KateSakharova
  committed
  f828cd5
- wip
  KateSakharova
  committed
  e3b8072
Commits on Apr 29, 2026
- Generate metadata CSV/TSV in modules instead of workflow body (#52)
  ochkalova
  authored
  d8beefc
- include topics
  KateSakharova
  committed
  006d953
- add READSUBMIT workflow
  ochkalova
  committed
  79c735b
- Merge branch 'dev' into feature/multiqc-citations
  KateSakharova
  committed
  121a75b
- fix links
  KateSakharova
  committed
  7a560d8
- different fixes
  KateSakharova
  committed
  d97a072
Commits on Apr 30, 2026
- fix bloody multiqc version
  KateSakharova
  committed
  689b785
- lint
  KateSakharova
  committed
  37e6886
- Template update for nf-core/tools version 4.0.2
  nf-core-bot
  committed
  96dee61
Commits on May 1, 2026
- fix wording and versions
  KateSakharova
  committed
  cf71ebf
Commits on May 5, 2026
- replace invalid Singularity container link
  ochkalova
  authored
  52ac46b
Commits on May 6, 2026
- update snaphots
  KateSakharova
  committed
  4d6dfbe
- revert multiqc container, die in hell!
  KateSakharova
  committed
  bb7e9ac
- snapshots
  KateSakharova
  committed
  80c4b08
- lint
  KateSakharova
  committed
  bbfcaf0
- Merge pull request #53 from nf-core/feature/multiqc-citations
  KateSakharova
  authored
  1c3e027
Commits on May 7, 2026
- Merge branch 'nf-core-template-merge-4.0.2' into dev
  vagkaratzas
  committed
  4a5d25b
- adding to template merge
  vagkaratzas
  committed
  de341c7
- m + s updates to latest
  vagkaratzas
  committed
  9deec0e
- replace fastavalidator
  KateSakharova
  committed
  6106618
- add failed to report
  KateSakharova
  committed
  5f581b7
Commits on May 11, 2026
- Latest template merge attempt (#62)
  
  vagkaratzas
  and
  nf-core-bot
  authored
  ee59e44
Commits on May 12, 2026
- delete incorrect config for reads test
  ochkalova
  committed
  0648352
- multiple fixes
  
  ochkalova
  and
  Copilot
  committed
  8cfcfd7
- Merge branch 'dev' into feat/readsubmit
  ochkalova
  authored
  e232200
- update multiqc in READSUBMIT
  
  ochkalova
  and
  Copilot
  committed
  651ca32
Commits on May 13, 2026
- Add arm64 configs (prep for biocontainers migration) -- updated snaps
  mberacochea
  committed
  51308e9
- nf-core linting - modules.json formatting
  mberacochea
  committed
  0892ccf
- Ignore container_configs when linting the pipeline
  mberacochea
  committed
  a95b77d
Commits on May 14, 2026
- fixes after review
  KateSakharova
  committed
  1c3f3bf
- Merge branch 'dev' into update-m+s
  KateSakharova
  authored
  1a293a6
- fixes after review
  KateSakharova
  committed
  f65ab00
- Regenerate tests snapshots
  mberacochea
  committed
  542f1c1
- Merge pull request #64 from nf-core/update-m+s
  mberacochea
  authored
  f3c1546
- remove --fasta-dir because it doesn't work for fastqs staged to different folders
  ochkalova
  committed
  00307d0
- disable publishDir for CREATE_READS_MANIFEST
  ochkalova
  committed
  5678294
Commits on May 18, 2026
Commits on May 19, 2026
Commits on Jun 4, 2026
- Update mgnify-pipelines-toolkit version to 1.5.1
  KateSakharova
  authored
  85541b5
- add single quotes for metadata values
  ochkalova
  committed
  b26b07d
- update pipeline metromap
  ochkalova
  committed
  486ae28
- update snapshots
  ochkalova
  committed
  dd7feec
- update containers
  ochkalova
  committed
  acf1ee0
- update samplesheet path
  ochkalova
  committed
  40db261
- update .nftignore
  ochkalova
  committed
  1d94d7d
- Merge pull request #58 from nf-core/feat/readsubmit
  ochkalova
  authored
  c744f44
Commits on Jun 10, 2026
- Delete test files from the repo and use nf-core datasets instead (#71)
  ochkalova
  authored
  b8cbf9b
Commits on Jun 19, 2026
- update genome_uploader
  KateSakharova
  committed
  573fa95
- add private
  KateSakharova
  committed
  1b906a4
- add to readme
  KateSakharova
  committed
  6733125
- lint
  KateSakharova
  committed
  475509a
- lint
  KateSakharova
  committed
  6daf3eb
Commits on Jun 23, 2026
- Update README.md
  
  KateSakharova
  and
  ochkalova
  authored
  ceaaa43
Commits on Jun 24, 2026
- wip fixing tests
  KateSakharova
  committed
  84f3cd1
- wip fixing tests
  KateSakharova
  committed
  17783b6
- wip fixing tests
  KateSakharova
  committed
  822f48e
- fix alias
  KateSakharova
  committed
  d4a66e8
- update logos
  KateSakharova
  committed
  24fb81e
- update logos
  KateSakharova
  committed
  03ea56d
- update logos
  KateSakharova
  committed
  1e18a1d
Commits on Jun 25, 2026
- lint
  KateSakharova
  committed
  6d5d510
- typos
  KateSakharova
  committed
  487b9ba
- lint
  KateSakharova
  committed
  511d3e6
- Merge pull request #73 from nf-core/hotfix/genome-upload
  KateSakharova
  authored
  6690021
- updated local modules
  KateSakharova
  committed
  10907de
- lint
  KateSakharova
  committed
  9304176
- add versions
  KateSakharova
  committed
  4e5b2ce
- fixes for release
  KateSakharova
  committed
  77f59c0
- change versions
  KateSakharova
  committed
  2f72cdc
- change versions in multiqc
  KateSakharova
  committed
  d9df7fb
Commits on Jun 26, 2026
- Modify registerstudy tests to generate seperate study_metadata.json files for each test to avoid a submission alias clash
  timrozday-mgnify
  committed
  6bfd1d7
Commits on Jun 27, 2026
- Update bin/submit_study.py
  
  KateSakharova
  and
  ochkalova
  authored
  ab8f212
- fix assembly test
  KateSakharova
  committed
  aa3aaa1
Commits on Jun 29, 2026
- Merge pull request #74 from nf-core/fix/conda-tests
  KateSakharova
  authored
  2789557
- rm dev from snapshots
  KateSakharova
  committed
  d31fd85
- fix typo
  KateSakharova
  committed
  4d05050
- Modify registerstudy tests to generate study metadata json files in temp directory using File.createTempFile()
  timrozday-mgnify
  committed
  eeb6c1f
- Merge pull request #77 from nf-core/bugfix/submission-alias-clash
  mberacochea
  authored
  bd677b6
- review containers
  KateSakharova
  committed
  b3adb48
- Merge pull request #75 from nf-core/1.0.0
  KateSakharova
  authored
  3b2ffb7
- fix container rename_fasta
  KateSakharova
  committed
  0d388a4
- fix release lint
  KateSakharova
  committed
  60b5a16
- update multiqc and nf-core subwf
  KateSakharova
  committed
  a411f30
Commits on Jun 30, 2026
- Update docs/CONTRIBUTING.md
  
  KateSakharova
  and
  ochkalova
  authored
  3b371d4
- test_full
  KateSakharova
  committed
  c44887a
- Merge pull request #78 from nf-core/1.0.0
  KateSakharova
  authored
  983909e
- try to fix download action
  KateSakharova
  committed
  bf5e09c
- lint
  KateSakharova
  committed
  8b64e77
- test
  KateSakharova
  committed
  2c5f597
Commits on Jul 1, 2026
- add credentials
  KateSakharova
  committed
  587d438
- test
  KateSakharova
  committed
  e294469
- fix folder creation in stub of GENOME_UPLOAD module
  ochkalova
  committed
  fa3c249
- fix branch definition for download_pipeline.yml
  ochkalova
  committed
  4d622f2
- clean up ENA_WEBIN and ENA_WEBIN_PASSWORD names usage
  ochkalova
  committed
  c9d5b8a
- create empty file in COUNT_RNA stub
  ochkalova
  committed
  c6a1fbe
- stricten empty file expectations for stub mode
  ochkalova
  committed
  eab0de8
- fix line index for 1 line file
  ochkalova
  committed
  27b7a4b
- ready to merge
  KateSakharova
  committed
  7714799
- Merge pull request #79 from nf-core/1.0.0
  KateSakharova
  authored
  327cee7
Commits on Jul 7, 2026
- fixes after review
  KateSakharova
  committed
  c105c5b
- fix
  KateSakharova
  committed
  ae4a2f4
- fix
  KateSakharova
  committed
  1f62e1e
- Merge pull request #82 from nf-core/1.0.0
  KateSakharova
  authored
  cf2cf3d
Commits on Jul 8, 2026
- polish contributions.md
  ochkalova
  committed
  340f3b2
- add limitations block
  ochkalova
  committed
  9692ab3
- refactor limitations block
  ochkalova
  committed
  4452cb8
- add scalability section to README.md
  ochkalova
  committed
  6bda9c7
- refactor contributing guidelines
  ochkalova
  committed
  9074e16
Commits on Jul 9, 2026
- start changing
  KateSakharova
  committed
  fe61978
- fix
  KateSakharova
  committed
  3e9998f
- update CONTRIBUTING.md to clarify testing requirements for ENA submission
  ochkalova
  committed
  44c38d9
- add some links
  KateSakharova
  committed
  67d436a
- update README.md to reference Methods documentation for metadata statistics and coverage calculation
  ochkalova
  committed
  b0343f4
- refactor methods documentation to clarify RNA presence detection and update metadata schema
  ochkalova
  committed
  f7f99b3
- add SVG pipeline metromap
  ochkalova
  committed
  36567f4
Commits on Jul 10, 2026
- update README.md Limitations to include issue tracking
  ochkalova
  committed
  c57e865
- update README.md to add a Table of Contents
  ochkalova
  committed
  f759e9c
- Move Data privacy section to usage.md
  ochkalova
  committed
  a7f6dd6
- use one format for tables with column descriptions in usage.md
  ochkalova
  committed
  81e64bd
- more fixes
  KateSakharova
  committed
  c11bab2
- slim Samplesheet descriptions in README to minimum
  ochkalova
  committed
  6aea0f8
- Add Table of Contents to usage.md
  ochkalova
  committed
  9394073
- move Submission Study section up in usage.md
  ochkalova
  committed
  cd8d99a
- Expand Requirements to include required pre-submissions
  ochkalova
  committed
  ae6b462
- Apply James' suggesstions in usage.md
  ochkalova
  committed
  bea141a
Commits on Jul 15, 2026
- restructure usage.md
  ochkalova
  committed
  59c7746
Commits on Jul 17, 2026
- polish usage.md structure and wording
  ochkalova
  committed
  b61853e
- update pipeline metromap
  ochkalova
  committed
  6d38ce3
- restructure README
  ochkalova
  committed
  2db92bd
- Add section for Third Party Assemblies (TPA) in usage.md
  ochkalova
  committed
  018d328
Commits on Jul 20, 2026
- Merge pull request #83 from nf-core/doc/limitations-scalability
  KateSakharova
  authored
  38b208d
Commits on Jul 21, 2026
- Merge branch '1.0.0' into fix/docs-review
  KateSakharova
  committed
  5a35079
- many fixes
  KateSakharova
  committed
  36700b4
- rename sample to id in samplesheet and add fields to meta directly from schema
  KateSakharova
  committed
  1a31a0f
Commits on Jul 22, 2026
- Fix prettier issues with docs/usage.md
  mberacochea
  committed
  f1228e7
- tidy up .map after review
  KateSakharova
  committed
  0a6e44b
- add null values as defaults for conditional args
  KateSakharova
  committed
  5b262bf
- update genome_uploader and fix regexp in multiqc
  KateSakharova
  committed
  54acdc9
- test multiqc config old version from 1.0.0 branch
  KateSakharova
  committed
  648ca9e
Commits on Jul 23, 2026
- change co-assembly and rna_presence to boolean
  KateSakharova
  committed
  edd594a
Commits on Jul 24, 2026
- Template update for nf-core/tools version 4.0.3
  nf-core-bot
  committed
  d3d61ad
- Remove vulnerable PR-comment artifact pattern
  nf-core-bot
  committed
  f00aebf
- Merge pull request #91 from nf-core/patch
  mashehu
  authored
  6cfb2b5
Commits on Jul 27, 2026
- change limits for coverage, completeness and contamination
  KateSakharova
  committed
  d0e42be
- Apply suggestion from @ochkalova
  
  KateSakharova
  and
  ochkalova
  authored
  774f69c
- Update subworkflows/local/genome_evaluation/main.nf
  
  KateSakharova
  and
  ochkalova
  authored
  99970b6
- Update conf/test_assembly_complete_metadata.config
  
  KateSakharova
  and
  ochkalova
  authored
  1a322b6
- Merge pull request #88 from nf-core/fix/meta_objects
  KateSakharova
  authored
  fb2db68
- remove nr from main workflow and add to taxonomy subwf
  KateSakharova
  committed
  2a0364c
- Update docs and schemas for better descriptions
  
  KateSakharova
  and
  ochkalova
  committed
  8af5f50
- Merge pull request #86 from nf-core/fix/docs-review
  KateSakharova
  authored
  645df17
Commits on Jul 30, 2026
- aligned docs and schemas
  KateSakharova
  committed
  b4a5d48
- docs polishing
  KateSakharova
  committed
  68a9c22
- Merge pull request #93 from nf-core/fix/unify-schema-and-docs
  KateSakharova
  authored
  4f98fff
- Merge branch '1.0.0' into nf-core-template-merge-4.0.3
  KateSakharova
  committed
  3a74926
- remove files_unchanged
  KateSakharova
  committed
  19067fb
- revert files_unchanged
  KateSakharova
  committed
  decd115
- Merge pull request #90 from nf-core/nf-core-template-merge-4.0.3
  KateSakharova
  authored
  5673e5b
- Merge branch 'dev' into 1.0.0
  KateSakharova
  authored
  fb3c3f1
- Revise resource settings guidance in usage documentation
  KateSakharova
  authored
  670bdc6
- Merge pull request #92 from nf-core/1.0.0
  KateSakharova
  authored
  361e07b

Commits

Commits on Mar 6, 2026

Commits on Mar 8, 2026

Commits on Mar 9, 2026

Commits on Mar 10, 2026

Commits on Mar 11, 2026

Commits on Mar 12, 2026

Commits on Mar 13, 2026

Commits on Mar 16, 2026

Commits on Mar 25, 2026

Commits on Mar 30, 2026

Commits on Apr 24, 2026

Commits on Apr 27, 2026

Commits on Apr 28, 2026

Commits on Apr 29, 2026

Commits on Apr 30, 2026

Commits on May 1, 2026

Commits on May 5, 2026

Commits on May 6, 2026

Commits on May 7, 2026

Commits on May 11, 2026

Commits on May 12, 2026

Commits on May 13, 2026

Commits on May 14, 2026

Commits on May 18, 2026