v1.1.4

What's Changed

• Avoid exiting due to i-ADHoRe warnings #46
• Add warning for negative distances during rate-adjustment #49
• Bugfix for exponential-lognormal mixture model: remove weight rounding during EM iterations #50
• Nextflow version in test_pipeline.yml is fixed to 21.10.6 for compatibility with DSL1 #50

Full Changelog: v1.1.3...v1.1.4

How to update to the latest release:

• To update the pipeline, run nextflow pull VIB-PSB/ksrates.
• To update the Docker image, run docker pull vibpsb/ksrates:latest.
• To update the Singularity image, remove the old image with rm vibpsb-ksrates-latest.img (this latter is located in cacheDir set in nextflow.config when using Nextflow). The next time the pipeline is launched, Nextflow will automatically pull the new image. To manually pull it, run instead singularity pull vibpsb-ksrates-latest.img docker://vibpsb/ksrates:latest in the same directory of the old image.

v1.1.3

What's Changed

• Add support for Nextflow version 22.03.0-edge and later in #43

Full Changelog: v1.1.2...v1.1.3

How to update to the latest release:

• To update the pipeline, run nextflow pull VIB-PSB/ksrates.
• To update the Docker image, run docker pull vibpsb/ksrates:latest.
• To update the Singularity image, remove the old image with rm vibpsb-ksrates-latest.img (this latter is located in cacheDir set in nextflow.config when using Nextflow). The next time the pipeline is launched, Nextflow will automatically pull the new image. To manually pull it, run instead singularity pull vibpsb-ksrates-latest.img docker://vibpsb/ksrates:latest in the same directory of the old image.

v1.1.2

What's Changed

• Added early checkpoint to catch syntax issues in the input Newick tree #35
• Added early checkpoint for input divergence colors in configuration file #36
• Added flexibility in filename and location of expert configuration file #37
• Added CITATION.cff #33
• Quick fix for test_pipeline.yml GitHub action file #34

Full Changelog: v1.1.1...v1.1.2

How to update to the latest release:

• To update the pipeline, run nextflow pull VIB-PSB/ksrates.
• To update the Docker image, run docker pull vibpsb/ksrates:latest.
• To update the Singularity image, remove the old image with rm vibpsb-ksrates-latest.img (this latter is located in cacheDir set in nextflow.config when using Nextflow). The next time the pipeline is launched, Nextflow will automatically pull the new image. To manually pull it, run instead singularity pull vibpsb-ksrates-latest.img docker://vibpsb/ksrates:latest in the same directory of the old image.

v1.1.1

What's Changed

• Update terminology in logging output #27
• Minor bug fix: plot-paralogs command can generate a missing directory if needed #28
• Reading ksrates version from ksrates/_version.py file #29
• Update push GitHub action to support ARM platforms #31
• Update requirement.txt with module versions #32

Full Changelog: v1.1...v1.1.1

How to update to the latest release:

• To update the pipeline, run nextflow pull VIB-PSB/ksrates.
• To update the Docker image, run docker pull vibpsb/ksrates:latest.
• To update the Singularity image, remove the old image with rm vibpsb-ksrates-latest.img (this latter is located in cacheDir set in nextflow.config when using Nextflow). The next time the pipeline is launched, Nextflow will automatically pull the new image. To manually pull it, run instead singularity pull vibpsb-ksrates-latest.img docker://vibpsb/ksrates:latest in the same directory of the old image.

v1.1

Merged pull requests:

• Condense, improve and clean up Nextflow logging #25
• LMM skipped if components are more than data points #24
• Nextflow pipeline removes leftover folders/files #23
• Update Usage docs (iterative ksrates runs) #22
• Improve compatibility between pipeline & cluster #21
• Increase memory for paralogsAnalyses NF process #20
• Add compact custom-made Nextflow error report #19
• Nextflow config update (autoMounts, envWhitelist) #18

How to update to the latest release:

• To update the pipeline, run nextflow pull VIB-PSB/ksrates.
• To update the Docker image, run docker pull vibpsb/ksrates:latest.
• To update the Singularity image, remove the old image with rm vibpsb-ksrates-latest.img (this latter is located in cacheDir set in nextflow.config when using Nextflow). The next time the pipeline is launched, Nextflow will automatically pull the new image. To manually pull it, run instead singularity pull vibpsb-ksrates-latest.img docker://vibpsb/ksrates:latest in the same directory of the old image.

v1.0

Merged pull requests:

• Rename parameters in configuration file #17
• Docs: interactive containers and WSL2 notes #16
• Reorder local installation steps in documentation #15
• Rename and describe headers in output files #14
• Fix dark gray color of anchor pair KDE #13
• Legend of ELMM models has handle pairs (tuples) #12
• Update axis labels (weighted data; fontsize) #11

v0.3

Merged pull requests:

• Rename parameters in configuration file #17
• Docs: interactive containers and WSL2 notes #16
• Reorder local installation steps in documentation #15
• Rename and describe headers in output files #14
• Fix dark gray color of anchor pair KDE #13
• Legend of ELMM models has handle pairs (tuples) #12
• Update axis labels (weighted data; fontsize) #11

v0.2

Full Changelog

Merged pull requests:

• Generate ortholog PDFs when data are unavailable #10
• Correct title position in elmm_species_peaks.pdf #9
• Ortholog distributiions PDF with 3 panels; no median #8
• PAML installation from source #7
• LMM convergence #6
• Anchor weights #5
• Ks plots without divergence lines have inner legend #4
• Update config.rst: mainly Nextflow config section #3
• Update Documentation (concept and input_output) #2
• Merge dev into master #1

v0.1

Initial release.