feat(islandpath): migrate to topic: versions tuple#11435
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@nf-core-bot fix linting |
| prefix = task.ext.prefix ?: "${meta.id}" | ||
| // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. | ||
| def VERSION = '1.0.6' | ||
| VERSION = '1.0.6' |
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| VERSION = '1.0.6' |
| args = task.ext.args ?: '' | ||
| prefix = task.ext.prefix ?: "${meta.id}" |
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These should still be def, don't know why you are changing this here.
HReed1
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Hey @SPPearce and @mribeirodantas — thanks for the reviews! I've pushed the fixes for both of your notes:
Let me know if we are good to go! |
| - '"1.0.6"': | ||
| type: string | ||
| description: The expression to obtain the version of the tool | ||
| 1.0.6: | ||
| type: string | ||
| description: The expression to obtain the version of the tool |
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These don't need to be duplicated.
| - '"1.0.6"': | ||
| type: string | ||
| description: The expression to obtain the version of the tool | ||
| 1.0.6: |
| tuple val(meta), path("*.gff") , emit: gff | ||
| path "Dimob.log" , emit: log | ||
| path "versions.yml" , emit: versions | ||
| // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. |
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Personally I think this is best above, on the line above the conda instruction.
- Replace versions.yml with val() topic: versions emission - Place // WARN: comment above conda directive - Add stub block for gff and log outputs - Add stub test with sanitizeOutput assertions - Migrate script test to findAll versions pattern - Remove // meta map comments from test inputs - Regenerate meta.yml, remove legacy versions output
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Hi @SPPearce @mribeirodantas — thanks for the thorough reviews! I've rebased against master and addressed all feedback in a single squashed commit: // WARN: placement — moved above the conda directive ✅ |
feat(islandpath): migrate to topic: versions, add stub block - Replace versions.yml with val() topic: versions emission - Place // WARN: comment above conda directive - Add stub block for gff and log outputs - Add stub test with sanitizeOutput assertions - Migrate script test to findAll versions pattern - Remove // meta map comments from test inputs - Regenerate meta.yml, remove legacy versions output
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Fixes #11323
Migrates the
islandpathmodule to use the standardizedtopic: versionschannel tuple emission, removes legacyversions.ymlgeneration, and incorporates strict-syntax validations.