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Recent Releases of arboratornf

arboratornf - 0.5.3

0.5.3 - 2025-08-08

Updated

- HTML
Published by sgsutcliffe 7 months ago

arboratornf - 0.5.2

0.5.2 - 2025-07-07

Updated

  • Updated the template ArborView html file assets/ArborView.html based on the the commit a826e1f of the html/table.html file in ArborView v.0.1.1 release. PR #48

  • Updated the arborator container (build 0 -> 1) which includes an update to the dependency of profile_dists. PR #48

- HTML
Published by sgsutcliffe 8 months ago

arboratornf - 0.5.1

0.5.1 - 2025-06-04

Fix

  • Updated the template ArborView html file assets/ArborView.html based on the the commit 046ed92 to the html/table.html file in ArborView v.0.1.0 that fixes rendering of plots. PR #45

- HTML
Published by sgsutcliffe 9 months ago

arboratornf - 0.5.0

0.5.0 - 2025-06-03

Updated

  • Updated ArborView to version 0.1.0. PR #43
    • assets/ArborView.html replaced with table.html
    • bin/inline_arborview.py replaced with fillin_data.py
    • line 32 of ARBOR_VIEW process outputs 0.1.0 now to software_versions.yml

Enhancement

  • locidex merge in 0.3.0 now performs the functionality of input_assure (checking sample name against MLST profiles). This allows arboratornf 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 9 months ago

arboratornf - 0.4.0

0.4.0 - 2025-05-26

Updated

Changed

  • Changed the arborator Nextflow module to print the versions of gas and profile_dists to make it easier to verify which versions of those software were used. PR #41

Removed

  • Removed matrix.pq (parquet) file in IRIDA Next JSON. PR #41

- HTML
Published by apetkau 9 months ago

arboratornf - Version 0.3.6

0.3.6 - 2025-05-05

Fix

  • Fixes the issue #38 metadata_partition containing a "." were leading to misnamed Arborview output files. PR #38

Added

  • /pipeline_info/software_versions.yml now added to the global files in the iridanext.output.json.gz to allow IRIDA-Next users access to software versions. PR #38

- HTML
Published by sgsutcliffe 10 months ago

arboratornf - Version 0.3.5

0.3.5 - 2025-04-16

Updated

  • Update the ArborView version to 0.0.8 (i.e. replace bin/inline_arborview.py with scripts/fillin_data.py and assets/ArborView.html with html/table.html) PR #33
  • Update the aborator container build which in turn updates the dependency, profile_dists, to version 1.0.4 PR #36

Changed

  • Changed the defaults for the arborator parameter --ar_thresholds from "10,9,8,7,6,5,4,3,2,1" to "100,50,25,20,15,10,5,0" PR #35

- HTML
Published by sgsutcliffe 10 months ago

arboratornf - Version 0.3.4

0.3.4 - 2025-03-20

Changed

  • Updated the build of the arborator container in order to update the genomic_address_service dependency to version 0.1.5. See PR #31.
  • Fixed some nf-core linting warnings and moved arborview.nf and maptotsv.nf modules to subfolders. See PR #31.
  • Removed unneeded input_check.nf. See PR #31.

- HTML
Published by apetkau 11 months ago

arboratornf - Version 0.3.3

0.3.3 - 2025-02-11

  • Updated the build of the arborator container in order to update the genomic_address_service dependency to version 0.1.4.

- HTML
Published by sgsutcliffe about 1 year ago

arboratornf - Version 0.3.2

0.3.2 - 2025-01-15

  • Updated the build of the arborator container in order to update the genomic_address_service dependency to version 0.1.3, which fixes an issue with branch lengths in Newick files PR 27.

- HTML
Published by apetkau about 1 year ago

arboratornf - 0.3.1

0.3.1 - 2024-11-05

CHANGED

  • Fixed the replacement of docker.userEmulation with docker.runOptions = '-u $(id -u):$(id -g)' that was causing a bug in Azure.
  • Modified documentation (missed in 0.3.0 release)

- HTML
Published by sgsutcliffe over 1 year ago

arboratornf - 0.3.0

2.3.0 - 2024-10-21

ADDED

  • Modified the template for input csv file to include a sample_name column in addition to sample in-line with changes to IRIDA-Next update as seen with the speciesabundance pipeline. (PR 23)

    • sample_name special characters 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

CHANGED

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

- HTML
Published by sgsutcliffe over 1 year ago

arboratornf - Version 0.2.0

0.2.0 - 2024-09-05

Changed

  • Upgraded locidex/merge to version 0.2.3 and updated input_assure.py and test data for compatibility with the new mlst.json allele file format.

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

arboratornf - 0.1.0

0.1.0 - 2024-08-20

Initial release of the arboratornf pipeline to be used for running Arborator under Nextflow.

Added

  • Basic functionality of Arborator.
  • Added support for metadata.
  • Automatically generate Arborator config files.
  • ArborView integration.

- HTML
Published by apetkau over 1 year ago