v2.1.0

What's Changed

PRs:

• Update docs expert file parameter list (#68)
• Update docs anchor pair Ks clustering (#69)
• Generate Ks plots using bottom-ranked reciprocally retained gene families (#72)
• Include paml4.9j file in vendor (#74)
• Bugfix paralogs_ks_multi command (#75)

Major updates:

• Fixed issue with paml4.9j installation: now the paml4.9.targz file is directly included in the ksrates repository
• Reciprocal retention pipeline can optionally generate the Ks plot for the bottom GFs. This is purely for comparison with the top GFs, it's not meaningful on its own and not intended for publication output.

Minor updates:

• Bugfix for paralogs-ks-multi command
• Updated online documentation about expert file and anchor pair Ks clustering

Full Changelog: v2.0.0...v2.1.0

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 Apptainer/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 apptainer pull vibpsb-ksrates-latest.img docker://vibpsb/ksrates:latest in the same directory of the old image.

v2.0.0

What's Changed

PRs:

• Update ksrates to version 2.0.0 (#63)
• Fixes before v2 release (GitHub actions, Dockerfile, fastcluster) (#67)

Major updates:

• Implemented the reciprocal retention pipeline along side the existing whole-paranome and anchor pair Ks analyses (more details in our preprint and in the documentation)
• Nextflow pipeline ported to DSL2 syntax

Minor updates:

• Containers only supported for linux/amd64 platform and no longer for linux/arm64
• Upgraded Python package versions in requirements.txt
• Output prints an automatic interpretation of the Ks plot, namely which species share which WGMs with the focal species
• New command orthologs_ks_cleanup: deletes all ortholog BLAST tables from ortholog_distributions directory to free disk space; to be executed manually
• New command paralogs_ks_multi: executes the paralog Ks estimation for all species present in the Newick tree instead than for only the focal species; to be executed manually
• Nextflow template configuration file contains scope profiles to set up containers
• Test pipeline CI action generates downloadable output (the whole test/rate_adjustment/elaeis directory) to allow inspection of error logs and output files

Full Changelog: v1.1.5...v2.0.0

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 Apptainer/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 apptainer pull vibpsb-ksrates-latest.img docker://vibpsb/ksrates:latest in the same directory of the old image.

v1.1.5

What's Changed

• Add customization of minimum anchor pair Ks value to be plotted and modelled #65 (requested in issue #64)
• Drop support for linux/arm64 when building and pushing Docker container to DockerHub (PR #66)

Full Changelog: v1.1.4...v1.1.5

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.

v1.1.4

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