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…tations, restructure subworkflows
Add gapseq media feature, update docs, and enhance pipeline visualiza…
Fix metabolic modeling defaults and resolve technical issues
…pipeline-specific config
Preparations for the first release
brovolia
changed the title
Normalize Python version to major.minor only
add possibilities to customize gapseq, fixed issue with multiple db downloads
adressing the comments
Addressing cooments
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 4.0.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
Automated security rollout could not apply this cleanly. Resolve the remaining conflict markers and *.rej files, then open a PR from 'patch' into 'dev'.
Remove vulnerable PR-comment artifact pattern
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 4.0.2. For more documentation on how to update your pipeline, please see the Synchronisation documentation. |
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❌ nf-test failed with latest Nextflow versionNote Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
See the full run for details. |
modified capruting python version to major.minor style
Points every test_*.config at the samplesheet.tsv hosted on nf-core/test-datasets (bacmodel branch) instead of the local assets/samplesheet.csv, matching test_full.config and the usual nf-core convention of keeping CI test inputs in the test-datasets repo. Requires the companion test-datasets PR that adds the optional medium_* columns to samplesheet.tsv, so test_carveme.config keeps exercising the gap-filling-on-a-medium code path.
Added possibility for user to specify already downloaded db
Merge pull request #2 from nf-core/dev
# Conflicts: # .nf-core.yml
Extending db options
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Added meta.yml for RENAME_GAPSEQ_XML
Fixed version consistency (1.0.0dev → 1.0.0)
Updated nf-core tools version (3.5.2 → 4.0.2)
Uncommented pipeline-specific config
Added rename/gapseq/xml to subworkflow
Disabled template_strings lint check