ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis - v2.2.3

What's Changed

• Changes to parsnp output handling by @evezeyl in https://github.com/NorwegianVeterinaryInstitute/ALPPACA/pull/133
• Changed how ParSNP handles output

Scientific Software - Peer-reviewed - Nextflow
Published by hkaspersen 7 months ago

ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis - v2.2.2

2.2.2 (2025-02-25)

Bug Fixes

• added semantic versioning, as of #121 (20fa052)

What's Changed

• Semantic versioning and process version updates by @hkaspersen in https://github.com/NorwegianVeterinaryInstitute/ALPPACA/pull/125

Full Changelog: https://github.com/NorwegianVeterinaryInstitute/ALPPACA/compare/v.2.3.2...v2.2.2

Scientific Software - Peer-reviewed - Nextflow
Published by hkaspersen 12 months ago

ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis - v.2.3.2

Patch 2.3.2 updates the version of Gubbins, fixed a bug for the input data to Parsnp (#117 ) and bumps the required version of Nextflow to 23.10.1. This update requires the user to add the following to their environment variables: export NXF_APPTAINER_HOME_MOUNT=true

If the user is not using APPTAINER, change this value to whatever else you are using, e.g. DOCKER.

Scientific Software - Peer-reviewed - Nextflow
Published by hkaspersen almost 2 years ago

ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis - v.2.3.1

Patch 2.3.1 comes with the following changes: - Updated the version of ParSNP to 2.0.3, as of issue https://github.com/NorwegianVeterinaryInstitute/ALPPACA/issues/112 - Updated Panaroo to version 1.3.4 - Bumped software versions in all reports - Added gffs as optional output with the command --output_gffs, as of issue https://github.com/NorwegianVeterinaryInstitute/ALPPACA/issues/113 - Fixed CI test disk space issue

Scientific Software - Peer-reviewed - Nextflow
Published by hkaspersen about 2 years ago

ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis - v.2.3.0

Version 2.3.0 is live! Several changes have been implemented:

• Added options for controlling sequence identity and length difference, issue https://github.com/NorwegianVeterinaryInstitute/ALPPACA/issues/108
• Added genepresenceabsence.tsv as output from Panaroo, issue https://github.com/NorwegianVeterinaryInstitute/ALPPACA/issues/107
• Downgraded the MLST tool to version 2.19.0 to get correct version of the Listeria mlst scheme, issue https://github.com/NorwegianVeterinaryInstitute/ALPPACA/issues/105
• Added columns in cgMLST hamming distance output for single-isolate metrics on missing and typed alleles, issue https://github.com/NorwegianVeterinaryInstitute/ALPPACA/issues/106
• Added a parameter for running IQ-Tree in fast mode, issue https://github.com/NorwegianVeterinaryInstitute/ALPPACA/issues/86
• Replaced prokka with bakta, issue https://github.com/NorwegianVeterinaryInstitute/ALPPACA/issues/54
• Set the seed parameter in gubbins, issue https://github.com/NorwegianVeterinaryInstitute/ALPPACA/issues/109

Scientific Software - Peer-reviewed - Nextflow
Published by hkaspersen about 2 years ago

ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis - cgMLST track

This version adds the cgMLST track to the pipeline! Run the track with --track cgmlst, check the Wiki for further information.

The following changes were implemented in addition: - Reports in all tracks were updated to the newest design where library and tool versions are reported at the bottom instead of the top to increase readability - Added input checks to all tracks, pipeline will fail correctly if input is missing in the run command

Scientific Software - Peer-reviewed - Nextflow
Published by hkaspersen almost 3 years ago

ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis - Version 2.1.0

This release adds the ANI track to the pipeline, using FastANI.

Scientific Software - Peer-reviewed - Nextflow
Published by hkaspersen almost 3 years ago

ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis - Version 2.0.3.1

Fixed bug where input file paths that didn't exist were ignored Added --seed parameter for pipeline reproducibility Updated manifest version

Scientific Software - Peer-reviewed - Nextflow
Published by hkaspersen about 3 years ago

ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis - Version 2.0.1

Minor update: - Made the QC module of the core gene track optional - Updated github action track tests to cover all three tracks

Scientific Software - Peer-reviewed - Nextflow
Published by hkaspersen over 3 years ago

ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis - v2.0.0

Major update following the JOSS review of ALPPACA. The pipeline has been changed to partially reflect the structure of NF-core pipelines. The following changes have been made:

• Pipeline is now executed directly using nextflow run, locally and directly from github
• Parameters are now supplied in the run command. Default parameter values are given in the nextflow.config
• Input changed to csv file containing the paths and sample names. The bin/generate_input.R script have been added to make it easy for users to generate this file
• Pipeline can be run by using singularity, docker, or conda as container handlers
• Example configuration files are supplied
• The pipeline now has test functionality, use with the test profile
• Added yml files for creating a run environment for the pipeline
• Updates to the wiki on how to run and configuration settings etc. to reflect the changes described above

Scientific Software - Peer-reviewed - Nextflow
Published by hkaspersen over 3 years ago

ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis - Version 1.0.4

Added local executor option, and some changes in how to execute the pipeline. Added test.sh script for testing the pipeline, as of issue #24.

Scientific Software - Peer-reviewed - Nextflow
Published by hkaspersen over 3 years ago

ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis - First full release

This is the first complete version of the ALPPACA pipeline. Changes include the addition of an html report for each track, and updates to tool versions. Additionally, the whole pipeline structure has been revised and updated to singularity. This makes it possible for off-SAGA use.

Scientific Software - Peer-reviewed - Nextflow
Published by hkaspersen almost 4 years ago

ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis - 0.2021.01.20

Minor updates to increase speed of pipeline and the addition of snp-filtering with snp-sites.

Scientific Software - Peer-reviewed - Nextflow
Published by hkaspersen about 5 years ago

ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis - 0.2020.11.24

First Zenodo release, and rename of pipeline

Scientific Software - Peer-reviewed - Nextflow
Published by hkaspersen about 5 years ago