Merge pending dependabot GitHub Actions bumps into dev#89
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Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5.2.0 to 6.1.0. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v5.2.0...v6.1.0) --- updated-dependencies: - dependency-name: actions/setup-python dependency-version: 6.1.0 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
…/actions/setup-python-6.1.0 Bump actions/setup-python from 5.2.0 to 6.1.0
license file and publication always refered to MPL-2.0, only the license attribute in the pyproject.toml file was wrong (MIT).
This script processes proteome data by parsing FASTA files, extracting transcripts, and writing splice files for species with multiple transcripts.
If external subprocesses such as mafft got killed (e.g. by SLURM) because of OOM, the main FastOMA python process did simply raise an Exception and terminated with exit code 1. This prevented nextflow from restarting it with more memory/time. We now report properly the exit code of Mafft and FastTree and exit the python code with the same exit code (stored in WrapperError)
use -profile slurm,large instead
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@copilot this should be merged into dev, not main! |
Addressed in 65c95ce. The workflow files ( |
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@copilot please rebase to current dev |
The file contents already reflect current git fetch origin dev
git rebase origin/dev
git push --force origin copilot/merge-all-requestsAlternatively, changing the PR's base branch from |
alpae
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Five open dependabot PRs (#84–#88) targeting
devhad accumulated without being merged. This consolidates all their changes into a single update targetingdev.Changes
nf-test.ymlactions/checkout→0c366fd(v6.0.2)actions/setup-python→a309ff8(v6.2.0)actions/setup-java→be666c2(v4 latest)conda-incubator/setup-miniconda→fc2d68f(v3.3.0)actions/upload-artifactv6 → v7dev:NFT_VER0.9.4, updated workdir paths (/tmp/nft-test), addedNXF_WORKandNXF_CONDA_CACHEDIRdocker-image.ymldevbranch version: multi-platform matrix build with separatelinux/amd64andlinux/arm64runners, digest-based push,mergejob for manifest list creation, andpublish-docjob for DockerHub description updatespublish-pypi-release.ymlactions/checkoutandactions/setup-pythonpinned to major version@v6🔒 GitHub Advanced Security automatically protects Copilot coding agent pull requests. You can protect all pull requests by enabling Advanced Security for your repositories. Learn more about Advanced Security.