transfer parameter definitions from deepmutscan.nf to nextflow.config #18
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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: 3.1.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
mashehu
approved these changes
Nov 19, 2025
| }, | ||
| "sliding_window_size": { | ||
| "type": "integer", | ||
| "description": "To flatten graphs in plots (e.g. GLOBAL_POS_BIASES_COUNTS function)", |
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| "description": "To flatten graphs in plots (e.g. GLOBAL_POS_BIASES_COUNTS function)", | |
| "description": "To flatten graphs in plots (e.g. `GLOBAL_POS_BIASES_COUNTS` function)", |
you can use markdown syntax for the description
| "mutagenesis_type": { | ||
| "type": "string", | ||
| "description": "Type of mutagenic primers. Choose from nnk, nns, max_diff_to_wt, custom. When using 'custom', also provide the parameter 'custom_codon_library'", | ||
| "description": "Type of mutagenic primers. Choose from nnk, nns, max_diff_to_wt, custom. When using 'custom', also provide the parameter 'custom_codon_library'. Default library is set to nnk", |
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| "description": "Type of mutagenic primers. Choose from nnk, nns, max_diff_to_wt, custom. When using 'custom', also provide the parameter 'custom_codon_library'. Default library is set to nnk", | |
| "description": "Type of mutagenic primers. Choose from nnk, nns, max_diff_to_wt, custom. When using 'custom', also provide the parameter 'custom_codon_library'.", |
we usually show the default value in all the relevant places already.
| "type": "string", | ||
| "format": "file-path", | ||
| "description": "Path to a comma-separated .txt file listing custom codons (e.g., 'AAA,AAC,AAG,...'). Required when mutagenesis_type is 'custom'." | ||
| "description": "Path to a comma-separated .txt file listing custom codons (e.g., 'AAA,AAC,AAG,...'). Required when mutagenesis_type is set to 'custom'." |
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is a comma-separated .txt file, not a .csv file?
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| "description": "Path to a comma-separated .txt file listing custom codons (e.g., 'AAA,AAC,AAG,...'). Required when mutagenesis_type is set to 'custom'." | |
| "description": "Path to a comma-separated .txt file listing custom codons (e.g., 'AAA,AAC,AAG,...'). Required when mutagenesis_type is set to `custom`." |
| "aimed_cov": { | ||
| "type": "integer", | ||
| "description": "aimed coverage (assuming equal spread) to visualize threshold in plots", | ||
| "default": 100 |
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one can set minimum and maximum values in json schema: https://json-schema.org/understanding-json-schema/reference/numeric#range , to help with some parameter validation
| "mutagenesis_type": { | ||
| "type": "string", | ||
| "description": "Type of mutagenic primers. Choose from nnk, nns, max_diff_to_wt, custom. When using 'custom', also provide the parameter 'custom_codon_library'", | ||
| "description": "Type of mutagenic primers. Choose from nnk, nns, max_diff_to_wt, custom. When using 'custom', also provide the parameter 'custom_codon_library'. Default library is set to nnk", |
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using enums simplifies parameter validation
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| "description": "Type of mutagenic primers. Choose from nnk, nns, max_diff_to_wt, custom. When using 'custom', also provide the parameter 'custom_codon_library'. Default library is set to nnk", | |
| "description": "Type of mutagenic primers. Choose from nnk, nns, max_diff_to_wt, custom. When using 'custom', also provide the parameter 'custom_codon_library'. Default library is set to nnk", | |
| "enum": ["nnk", "nns", "max_diff_to_wt", "custom"], |
| "type": "boolean", | ||
| "default": false, | ||
| "description": "Enable DiMSum execution." | ||
| "description": "Run DiMSum for fitness/functionality scores from grwoth-based selection input & output samples" |
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| "description": "Run DiMSum for fitness/functionality scores from grwoth-based selection input & output samples" | |
| "description": "Run DiMSum for fitness/functionality scores from growth-based selection input & output samples" |
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).