Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of gasclustering

gasclustering - 0.7.2

0.7.2 - 2025-08-08

Updated

- HTML
Published by sgsutcliffe 7 months ago

gasclustering - 0.7.1

0.7.1 - 2025-06-28

Updated

  • Update profile_dists to v.1.0.8. PR #54
  • Update ArborView to v.0.1.1. PR #55

- HTML
Published by sgsutcliffe 8 months ago

gasclustering - 0.7.0

0.7.0 - 2025-06-06

Updated

  • Updated ArborView to version 0.1.0. PR #52
    • assets/ArborView.html replaced with table.html
    • bin/inline_arborview.py replaced with fillin_data.py
    • The ARBOR_VIEW process now outputs the version of ArborView (0.1.0) to software_versions.yml
  • Updated nf-core module custom_dumpsoftwareversions to latest version (commit 05954dab2ff481bcb999f24455da29a5828af08d). PR #52
  • Updated nf-core linting and some of the nf-core GitHub actions to the latest versions. PR #52

- HTML
Published by apetkau 9 months ago

gasclustering - 0.6.3

0.6.3 - 2025-05-26

Fixed

  • Add a Ubuntu container for COPY_FILE to run on Azure. PR #50

- HTML
Published by sgsutcliffe 9 months ago

gasclustering - 0.6.2

0.6.2 - 2025-05-26

Fixed

  • Fixed issue with dupilcate MLST JSON file names as input. PR #48.

- HTML
Published by apetkau 9 months ago

gasclustering - 0.6.1

0.6.1 - 2025-05-16

Fixed

  • Patched issue with LOCIDEX_MERGE input channel (path instead of val) causing issues with filesystems. PR #46

- HTML
Published by sgsutcliffe 10 months ago

gasclustering - 0.6.0

0.6.0 - 2025-05-14

Updated

  • Updated genomic address service to v.0.2.0 PR #44
  • Updated profile_dists to v.1.0.5 PR #44
  • Updated ArborViewto v.0.0.8 using files from arboratornf PR #33. PR #44

Enhancement

  • locidex merge in 0.3.0 now performs the functionality of input_assure (checking sample name against MLST profiles). This allows gasclustering to remove input_assure so that the MLST JSON file is read only once, and no longer needs to re-write with correction. PR #44
  • Added a pre-processing step to the input of LOCIDEX_MERGE that splits-up samples, into batches (default batch size: 100), to allow for LOCIDEX_MERGE to be run in parallel. To modify the size of batches use the parameter --batch_size n. PR #44

- HTML
Published by sgsutcliffe 10 months ago

gasclustering - 0.5.0

0.5.0 - 2025-04-04

Changed

  • Changed file extensions (.text -> .tsv) of output files from GAS_MCLUSTER and PROFILE_DISTS found in the iridanext.output.json. Output files are now compatiable with file preview feature in IRIDA Next. PR #40

Updated

  • Update the profile_dist version to 1.0.4. PR 41
  • Update the ArborView version to 0.0.8 (i.e. replace assets/ArborView.html with html/table.html) PR 42

- HTML
Published by sgsutcliffe 11 months ago

gasclustering - 0.4.3

0.4.3 - 2025-03-17

Changed

  • Updating the version of GAS container from 0.1.4 -> 0.1.5. See PR #37.
  • Updating the version of locidex container from 0.2.3 -> 0.3.0. See PR #37.
  • Updating the version of profile_dists container from 1.0.2 -> 1.0.3. See PR #37.
  • Fixed some nf-core linting warnings and moved arborview.nf module to subfolder. See PR #37.

- HTML
Published by apetkau 12 months ago

gasclustering - Version 0.4.2

0.4.2 - 2025-02-11

Changed

Updating the version of GAS container from 0.1.3 -> 0.1.4

- HTML
Published by sgsutcliffe about 1 year ago

gasclustering - Version 0.4.1

0.4.1 - 2024-12-23

Changed

  • Updated the version of GAS container 0.1.1 -> 0.1.3 used by gasclustering.

- HTML
Published by sgsutcliffe about 1 year ago

gasclustering - Version 0.4.0

0.4.0 - 2024-11-07

Changed

  • Added the ability to include a sample_name column in the input samplesheet.csv. Allows for compatibility with IRIDA-Next input configuration. (PR #31)

    • sample_name special characters (non-alphanumeric with exception of "" and ".") will be replaced with `""`
    • If no sample_name is supplied in the column sample will be used
    • To avoid repeat values for sample_name all sample_name values will be suffixed with the unique sample value from the input file

Bug fix

  • Fixed linting issues in CI caused by nf-core 3.0.1

- HTML
Published by sgsutcliffe over 1 year ago

gasclustering - Version 0.3.0

0.3.0 - 2024-09-10

Changed

  • Upgraded profile_dist container to version 1.0.2
  • Upgraded locidex/merge to version 0.2.3 and updated input_assure and test data for compatibility with the new mlst.json allele file format.
  • Aligned container registry handling in configuration files and modules with phac-nml/pipeline-standards

This pipeline is now compatible only with output generated by Locidex v0.2.3+ and Mikrokondo v0.4.0+.

- HTML
Published by kylacochrane over 1 year ago

gasclustering - Version 0.2.0

0.2.0 - 2024-06-26

Added

  • Support for mismatched IDs between the samplesheet ID and the ID listed in the corresponding allele file.

Changed

  • Updated ArborView to v0.0.7-rc1.

Fixed

  • The scaled distance thresholds provided when using --pd_distm scaled and --gm_thresholds are now correctly understood as percentages in the range [0.0, 100.0].

- HTML
Published by emarinier over 1 year ago

gasclustering - Version 0.1.0

0.1.0 - 2024-05-28

Initial release of the Genomic Address Service Clustering pipeline to be used for distance-based clustering of cg/wgMLST data.

Added

  • Input of cg/wgMLST allele calls produced from locidex.
  • Output of a dendrogram, cluster codes, and visualization using profile_dists, gas mcluster, and ArborView.

- HTML
Published by apetkau almost 2 years ago