Update amulety modules #9674
Update amulety modules #9674
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Joon-Klaps
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Joon-Klaps
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There are some rules on deprecating modules. https://nf-co.re/docs/guidelines/components/module_deprecation
Think it might be better to make a amulety2? What do you think?
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Ah thanks, I wasn't aware of this. I don't think it's needed to use AMULETY2, since the deprecated commands are no longer available. Instead of deleting the old modules I will deprecate them. |
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Hi @Joon-Klaps I've deprecated the old modules now instead of just removing them. Let me know if the PR now looks good to you when you have a minute |
Joon-Klaps
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Minor suggestions, everything else looks good to me!
| - chain: | ||
| type: string | ||
| description: | | ||
| The chain to use for the embeddings. Can be either 'H' (high diversity chain: BCR heavy or TCR beta or delta), | ||
| 'L' (low diversity chain: BCR light or TCR alpha or gamma) or 'HL' (BCR heavy + light, and TCR alpha + beta or gamma + delta). |
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| - chain: | |
| type: string | |
| description: | | |
| The chain to use for the embeddings. Can be either 'H' (high diversity chain: BCR heavy or TCR beta or delta), | |
| 'L' (low diversity chain: BCR light or TCR alpha or gamma) or 'HL' (BCR heavy + light, and TCR alpha + beta or gamma + delta). | |
| - chain: | |
| type: string | |
| description: | | |
| The chain to use for the embeddings. Can be either 'H' (high diversity chain: BCR heavy or TCR beta or delta), | |
| 'L' (low diversity chain: BCR light or TCR alpha or gamma) or 'HL' (BCR heavy + light, and TCR alpha + beta or gamma + delta). | |
| enum: ['L', 'H', 'HL'] |
| type: file | ||
| description: TSV with embeddings of BCR or TCR amino acid sequences. | ||
| pattern: "*.tsv" | ||
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| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" |
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You don't suspect a filename clash, as both input and output files are tsv files? If so, here is the suggestion
| def prefix = task.ext.prefix ?: "${meta.id}" | |
| def prefix = task.ext.prefix ?: "${meta.id}" | |
| if ("${tsv}" == "${prefix}.tsv") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" | |
| """ | ||
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| stub: | ||
| def prefix = task.ext.prefix ?: "${meta.id}" |
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| def prefix = task.ext.prefix ?: "${meta.id}" | |
| def prefix = task.ext.prefix ?: "${meta.id}" | |
| if ("${input}" == "${prefix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" | |
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Update amulety modules: in amulety>=2.0 the command syntax and subcommands have changed and I updated the nf-core modules are accordingly.