snvphylnfc - 2.3.1

2.3.1 - 2025-08-08

Updated

• Upgraded ArborView to v.0.1.2. Update assets/AborView.html in pipeline with html/table.html. PR #36

- HTML
Published by sgsutcliffe 11 months ago

snvphylnfc - 2.3.0

2.3.0 - 2025-06-09

Added

• Added software_versions.yml to the files included within the iridanext.output.json.gz file. PR #34

Updated

• Updated ArborView to version 0.1.0. PR #34
  • 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 #34
• Updated nf-core module cat_cat to latest version (commit 05954dab2ff481bcb999f24455da29a5828af08d). PR #34
• Updated nf-core linting and some of the nf-core GitHub actions to the latest versions. PR #34

- HTML
Published by apetkau about 1 year ago

snvphylnfc - 2.2.2

2.2.2 - 2025/04/14

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 #31

- HTML
Published by sgsutcliffe about 1 year ago

snvphylnfc - 2.2.1

2.2.1 - 2025/03/20

Changed

• Increased resources for VERIFYING_MAP_Q from process_single to process_high for processing larger numbers of samples. See PR #29.
• Increased resources for PHYML from process_low to process_medium for processing larger numbers of samples. See PR #29.
• Increased resources for SMALT_MAP from process_single to process_medium for processing larger numbers of samples faster. See PR #29.
• Increased resources for SORT_INDEX_BAMS from process_low to process_medium for processing larger numbers of samples and included command option for using multiple threads. See PR #29.
• Updated nf-core lint version to 3.2.0. See PR #29.
• Fixed some nf-core linting warnings and moved arborview.nf module to subfolders. See PR #29.

- HTML
Published by apetkau over 1 year ago

snvphylnfc - 2.2.0

2.2.0 - 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 26)

  • 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

snvphylnfc - 2.1.1

2.1.1 - 2024/08/21

CHANGED

• Container registry for aborview switched from docker.io to quay.io/biocontainers (python:3.11.6 to python:3.12)

- HTML
Published by sgsutcliffe almost 2 years ago

snvphylnfc - 2.1.0

2.1.0 - 2024/07/09

Added

• Support for including contextual metadata in the input samplesheet
• ArborView HTML app functionality for viewing dendograms with contextual metadata

- HTML
Published by kylacochrane almost 2 years ago

snvphylnfc - 2.0.2

2.0.2 - 2024/05/21

Added

• Support for compressed (GZIP-formatted) reference files.

- HTML
Published by emarinier about 2 years ago

snvphylnfc - 2.0.1

2.0.1 - 2024/02/23

Changed

• Pinned Nextflow plugins to specific versions (nf-validation@1.1.3 and nf-iridanext@0.2.0)

- HTML
Published by kylacochrane over 2 years ago

snvphylnfc - 2.0.0

2.0.0 - 2024/02/14

Added

• The initial release of phac-nml/snvphylnfc as a Nextflow pipeline follwing nf-core pipeline standards.

Changed

• Migrated SNVPhyl to a Nextflow pipeline.
• Updated the major SNVPhyl release version from 1 to 2 in order to reflect the migration from a Galaxy-based pipeline to a Nextflow-based pipeline.

- HTML
Published by emarinier over 2 years ago