Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Version 0.1.0 Release #18

Merged
merged 139 commits into from
Jun 28, 2024
Merged
Changes from 1 commit
Commits
Show all changes
139 commits
Select commit Hold shift + click to select a range
4a32688
updated tracked test data
Apr 2, 2024
377b998
Merge pull request #3 from phac-nml/workflow
mattheww95 Apr 2, 2024
3ef255b
Created initial workflow
Apr 2, 2024
40e41c8
added initial unit tests
Apr 2, 2024
f4d2887
removed module tests
Apr 2, 2024
bebcbb3
updated expected clusters path
Apr 2, 2024
2b8de97
updated test configs
Apr 2, 2024
e8a7373
updated nftest.config
Apr 3, 2024
b64bb3d
updated test outpu path
Apr 3, 2024
f1756e9
updated test output paths
Apr 3, 2024
7c1e516
fixed test data line endings
Apr 3, 2024
bdfe6c3
updated paths to expected input files
Apr 3, 2024
1515c37
updated test conf file input paths
Apr 3, 2024
fbd6117
updated params in test configs
Apr 3, 2024
ca448b5
updated schema, and test file line endings
Apr 3, 2024
6893ece
updated schema types
Apr 3, 2024
141b040
Ran prettier
Apr 3, 2024
7ce6e9f
updated function data types
Apr 3, 2024
dccc794
Merge pull request #4 from phac-nml/workflow
mattheww95 Apr 4, 2024
be8a632
Update gas_nomenclature.nf
mattheww95 Apr 5, 2024
f249833
Merge pull request #5 from phac-nml/fix-prepFilePaths
apetkau Apr 5, 2024
1e554dd
Updated samplesheet to include 'address' column
kylacochrane May 6, 2024
adfe193
Updated locidex_merge_ref to include all samples, including new query…
kylacochrane May 6, 2024
2a79100
Updated expected test results to accomdate all samples in reference
kylacochrane May 6, 2024
1142788
EC error fix
kylacochrane May 6, 2024
b5ee774
New module to filter out the new query addresses
kylacochrane May 6, 2024
d6f315b
Added nf-iridanext plugin
kylacochrane May 7, 2024
69dd10a
EC error fix
kylacochrane May 7, 2024
7a9eeb9
Adding a basic solution for identifying when sample ID's do not match…
kylacochrane May 8, 2024
3ec26e2
Update query filtering process name and add versions
kylacochrane May 15, 2024
d80f347
Updated linting to resolve issues
kylacochrane May 15, 2024
5aaaa3b
Fixed another linting issue
kylacochrane May 15, 2024
272c8ac
Fixing linting issues, for real this time
kylacochrane May 15, 2024
3874698
Merge branch 'filter-new-addresses' into input_check
kylacochrane May 15, 2024
b9367ec
Add new modules/processes: INPUT_CHECK, SAMPLE_FILTER, ERROR_REPORT
kylacochrane May 15, 2024
a7ca9b0
Add corresposonding python scripts; remove unused scripts
kylacochrane May 15, 2024
d0829d4
Update iridanext.config to include error_reports
kylacochrane May 15, 2024
c616b5b
Updated workflow
kylacochrane May 15, 2024
0059a9b
Uploading files for new integration tests
kylacochrane May 16, 2024
fd90fa1
Added new test and configuration files; fixed EC issues
kylacochrane May 16, 2024
df524f6
Improvements to the FILTER_QUERY module
kylacochrane May 16, 2024
9e50182
EC fix
kylacochrane May 16, 2024
6cf40c3
Merge branch 'filter-new-addresses' into input_check
kylacochrane May 16, 2024
e4d5031
Fixed discrepancy with previous merged from filter-new-addresses into…
kylacochrane May 16, 2024
5bfe569
Remove left-overs from pipeline template
kylacochrane May 16, 2024
b4e8d25
Fixed linting issue with modules.config
kylacochrane May 16, 2024
cf37bfe
Merge INPUT_CHECK and ERROR_REPORT into one module
kylacochrane May 16, 2024
11f7be9
Fixed input_check.py
kylacochrane May 16, 2024
2f674ec
Update iridanext.config
kylacochrane May 16, 2024
5456aa7
Updated workflow to filter sample inputs and removed corresponding mo…
kylacochrane May 17, 2024
f71d0f3
Merge branch 'input_check' into add_tests
kylacochrane May 17, 2024
40211de
Update main.nf.test to align with changes from input-check branch
kylacochrane May 17, 2024
7feaee8
Updated main.nf.test
kylacochrane May 17, 2024
7f77c9d
Merge pull request #10 from phac-nml/add_tests
kylacochrane May 21, 2024
4589456
Reverted changes to nf-core module
kylacochrane May 21, 2024
9748287
Improvement to workflow
kylacochrane May 21, 2024
131af6f
Updated workflow
kylacochrane May 21, 2024
16901d1
Merge pull request #9 from phac-nml/input_check
kylacochrane May 22, 2024
ff4982a
Merge pull request #8 from phac-nml/filter-new-addresses
kylacochrane May 22, 2024
88c1a7f
Merge pull request #7 from phac-nml/references-all
kylacochrane May 22, 2024
74fb861
Merge pull request #6 from phac-nml/samplesheet-update
kylacochrane May 22, 2024
b1c888a
Update URLs in test samplesheets
kylacochrane May 22, 2024
928ca15
Add a module to partition reference sample addresses into hierarchica…
kylacochrane May 27, 2024
d2f8a0b
Update workflow to generated expected_clusters file
kylacochrane May 27, 2024
2320029
Update test.config
kylacochrane May 27, 2024
fef02bc
Update gas-call expected_results.txt following modification of sample…
kylacochrane May 27, 2024
28c098a
Fixed typo
kylacochrane May 27, 2024
de705f6
Update parameters for profile_dists and gas_call; Add/update descript…
kylacochrane May 27, 2024
76c6980
Remove pd_force from nextflow.config
kylacochrane May 27, 2024
e9e14f0
Removed pd_force argument from profile_dists/main.nf
kylacochrane May 27, 2024
43a0b41
update documentation
kylacochrane May 27, 2024
f01e12c
Update gm_delimiter parameter
kylacochrane May 27, 2024
dabbdec
Fixed defaults for gm_delimiter
kylacochrane May 27, 2024
4a199de
Fix whitespace
kylacochrane May 27, 2024
1019492
Update CLUSTER_FILE to split on gm_delimiter
kylacochrane May 28, 2024
19a1679
Raise exception if sample levels are different
kylacochrane May 29, 2024
2758cd0
Updated cluster_file process to use 'error' instead of 'throw Exception'
kylacochrane May 30, 2024
bd0cd1a
Added a cluster_file process test to evaluate samples with different …
kylacochrane May 30, 2024
6b7243a
Add clustering method
kylacochrane Jun 4, 2024
e32f5d2
Comment removed from gas-call main.nf
kylacochrane Jun 4, 2024
20f5522
Removed padding in cluster_file process
kylacochrane Jun 6, 2024
b449215
nextflow.config comment clean up
kylacochrane Jun 6, 2024
be3ba26
Revise 'input_check' to 'input_assure'; enforce JSON key alteration t…
kylacochrane Jun 6, 2024
95e40f6
Remove id_match from meta
kylacochrane Jun 7, 2024
9e20417
Fix linting
kylacochrane Jun 7, 2024
deb4349
Updated error_message from input_assure
kylacochrane Jun 7, 2024
358175e
fix: correctly escape delimiter in CLUSTER_FILE process
kylacochrane Jun 7, 2024
b4cbd03
Add check to main.nf.test to assert query profile is merged
kylacochrane Jun 7, 2024
6691dea
Added success case to cluster_file process test
kylacochrane Jun 7, 2024
a1b3685
Update README and USAGE documents
kylacochrane Jun 7, 2024
04ee4fd
Remove the --pd_outfmt paramater
kylacochrane Jun 7, 2024
07fe2c6
Update python script name to match process: input_assure.py
kylacochrane Jun 10, 2024
23c1397
Add 'fair = true' to input_assure process in modules.config for repro…
kylacochrane Jun 10, 2024
c7252cf
Update input_assure.py to include additional check for multiple keys
kylacochrane Jun 10, 2024
f7ed9d3
Fixed linting issues
kylacochrane Jun 10, 2024
4acdb8c
Merge pull request #11 from phac-nml/expected-clusters
kylacochrane Jun 10, 2024
9be4562
Resolved conflicts between dev and update-parameters
kylacochrane Jun 11, 2024
eedf303
Merge pull request #12 from phac-nml/update-parameters
kylacochrane Jun 11, 2024
6d76d50
Update filter_query to accomodate multiple queries
kylacochrane Jun 11, 2024
59f4d17
Add test for multiple_queries and supporting files
kylacochrane Jun 11, 2024
0742c50
Implement 'fair true' in input_check to insure consistent ordering of…
kylacochrane Jun 11, 2024
d1c9809
Update file path in samplesheet
kylacochrane Jun 11, 2024
07b6c3c
Added missing expected test file
kylacochrane Jun 11, 2024
15b7090
Changed cluster_file output filename for clarity
kylacochrane Jun 12, 2024
608f4d0
Merge pull request #14 from phac-nml/update-filter_query
kylacochrane Jun 12, 2024
7d93226
Merge 'dev' into 'input_assure
kylacochrane Jun 12, 2024
7592bd3
Resolve conflicts between dev and input_assure
kylacochrane Jun 12, 2024
3266330
Add test with gzipped MLST JSON file
kylacochrane Jun 12, 2024
82c3a0d
Added test for mismatched IDs
kylacochrane Jun 12, 2024
0017090
Update paths in samplesheet
kylacochrane Jun 12, 2024
3f181eb
Fix EC issues
kylacochrane Jun 12, 2024
1f52529
Fix EC issues
kylacochrane Jun 12, 2024
ec347e4
Removed unexpected character (#) in main.nf.test
kylacochrane Jun 12, 2024
7c1b5dc
Add test data for multiple keyed JSON file
kylacochrane Jun 13, 2024
8e8ffa4
Tests added to handle when there are multiple sample entries (keys) i…
kylacochrane Jun 13, 2024
7909673
Updated input_assure to identify when MLST JSON is empty. Added corre…
kylacochrane Jun 13, 2024
da8c829
EC issue fix
kylacochrane Jun 13, 2024
6642b72
Create a new JSON output file in input_assure
kylacochrane Jun 13, 2024
348fe95
Ensure MLST JSON files from input_assure are gzipped
kylacochrane Jun 14, 2024
11167bd
Merge pull request #13 from phac-nml/input_assure
kylacochrane Jun 14, 2024
327e46b
Update samplesheet paths to mlst.json reports
kylacochrane Jun 14, 2024
95c0f5c
Add gas parameter tests
kylacochrane Jun 17, 2024
0b2ba27
Add test for hash-missing
kylacochrane Jun 17, 2024
27ff579
Added test when counting missing data
kylacochrane Jun 17, 2024
23ec449
Added test for removing missing loci
kylacochrane Jun 17, 2024
01b1e4b
Added tests with pd_columns
kylacochrane Jun 17, 2024
b08a816
Update documentation
kylacochrane Jun 17, 2024
cdbe9ef
Update CHANGELOG.md
kylacochrane Jun 19, 2024
63e69b3
Update workflow to allow gm_threshold to be single integers
kylacochrane Jun 19, 2024
c57ef6c
Add success tests for different thresholds
kylacochrane Jun 19, 2024
cc8b033
Fix error in main_gm_threshold.nf.test
kylacochrane Jun 19, 2024
950704c
Merge pull request #15 from phac-nml/add_tests
kylacochrane Jun 20, 2024
1ed30b8
Updating tests and documentation to correct 'scaled' distances
kylacochrane Jun 24, 2024
00a97c9
Added the expected test data files for scaled distances
kylacochrane Jun 24, 2024
d2e2c80
Updated README to expand on GAS thresholds and linkage methods
kylacochrane Jun 26, 2024
c6d4ba6
Merge pull request #16 from phac-nml/update_scaled
kylacochrane Jun 27, 2024
df7c748
Updating docs for release
kylacochrane Jun 27, 2024
32b88c5
Add link to release to CHANGELOG.md
kylacochrane Jun 27, 2024
08582c8
Merge pull request #17 from phac-nml/release_version
kylacochrane Jun 28, 2024
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
Update CHANGELOG.md
  • Loading branch information
kylacochrane committed Jun 19, 2024
commit cdbe9ef8b5216a38abaa77aa314d9ebb47a0c12f
34 changes: 5 additions & 29 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -3,39 +3,15 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## In-development
## 0.1.0 - 2024/06/18

## 1.0.5 - 2024/06/17

- Updated modules to include:

- `input_assure`: Performs a validation check on the samplesheet inputs to ensure that the sampleID precisely matches the MLST JSON key and enforces necessary changes where discrepancies are found.
- `cluster_file`: Generates the expected_clusters.txt file from reference sample addresses for use in GAS_call.
- `filter_query`: Filters and generates a csv file containing only the cluster addresses for query samples.

- Pinned nf-iridanext plugin
- Added tests for the full pipeline, independant modules, and input parameters
- Updated documentation and configuration files

## 1.0.3 - 2024/02/23

- Pinned [email protected] plugin

## 1.0.2 - 2023/12/18

- Removed GitHub workflows that weren't needed.
- Adding additional parameters for testing purposes.

## 1.0.1 - 2023/12/06

Allowing non-gzipped FASTQ files as input. Default branch is now main.

## 1.0.0 - 2023/11/30

Initial release of phac-nml/gasnomenclature, created with the [nf-core](https://nf-co.re/) template.
Initial release of the Genomic Address Nomenclature pipeline to be used to assign cluster addresses to samples based on an existing cluster designations.

### `Added`

- Input of cg/wgMLST allele calls produced from [locidex](https://github.com/phac-nml/locidex).
- Output of assigned cluster addresses for any **query** samples using [profile_dists](https://github.com/phac-nml/profile_dists) and [gas call](https://github.com/phac-nml/genomic_address_service).

### `Fixed`

### `Dependencies`