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@@ -185,6 +185,7 @@ We thank the following people for their extensive assistance in the development | |
| **TODO** | ||
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| <!-- TODO nf-core: If applicable, make list of people who have also contributed --> | ||
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| Nagarajan Paramasivam @NagaComBio [email protected] | ||
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| ## Contributions and Support | ||
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@@ -193,7 +194,6 @@ If you would like to contribute to this pipeline, please see the [contributing g | |
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| ## Citations | ||
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| <!-- If you use nf-platypusindelcalling for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) --> | ||
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| <!-- TODO nf-core: Add bibliography of tools and data used in your pipeline --> | ||
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| @@ -1,54 +1,54 @@ | ||
| { | ||
| "$schema": "http://json-schema.org/draft-07/schema", | ||
| "$id": "https://raw.githubusercontent.com/ghga-de/nf-platypusindelcalling/master/assets/schema_input.json", | ||
| "title": "nf-platypusindelcalling pipeline - params.input schema", | ||
| "description": "Schema for the file provided with params.input", | ||
| "type": "array", | ||
| "items": { | ||
| "type": "object", | ||
| "properties": { | ||
| "sample": { | ||
| "type": "string", | ||
| "pattern": "^\\S+$", | ||
| "errorMessage": "Sample name must be provided and cannot contain spaces" | ||
| }, | ||
| "tumor": { | ||
| "type": "string", | ||
| "pattern": "^\\S+\\.bam$", | ||
| "errorMessage": "BAM file for tumors must be provided'" | ||
| }, | ||
| "tumor_index": { | ||
| "type": "string", | ||
| "pattern": "^\\S+\\.bai$", | ||
| "errorMessage": "BAI file matching to BAM for tumors must be provided'" | ||
| }, | ||
| "control": { | ||
| "errorMessage": "BAM file for as control matching to tumor, if there is", | ||
| "anyOf": [ | ||
| { | ||
| "type": "string", | ||
| "pattern": "^\\S+\\.bam$" | ||
| }, | ||
| { | ||
| "type": "string", | ||
| "maxLength": 0 | ||
| } | ||
| ] | ||
| }, | ||
| "control_index": { | ||
| "errorMessage": "BAI file matching to BAM for as control matching to tumor, if there is", | ||
| "anyOf": [ | ||
| { | ||
| "type": "string", | ||
| "pattern": "^\\S+\\.bai$" | ||
| }, | ||
| { | ||
| "type": "string", | ||
| "maxLength": 0 | ||
| } | ||
| ] | ||
| } | ||
| }, | ||
| "required": ["sample", "tumor", "tumor_index"] | ||
| } | ||
| "$schema": "http://json-schema.org/draft-07/schema", | ||
| "$id": "https://raw.githubusercontent.com/ghga-de/nf-platypusindelcalling/master/assets/schema_input.json", | ||
| "title": "nf-platypusindelcalling pipeline - params.input schema", | ||
| "description": "Schema for the file provided with params.input", | ||
| "type": "array", | ||
| "items": { | ||
| "type": "object", | ||
| "properties": { | ||
| "sample": { | ||
| "type": "string", | ||
| "pattern": "^\\S+$", | ||
| "errorMessage": "Sample name must be provided and cannot contain spaces" | ||
| }, | ||
| "tumor": { | ||
| "type": "string", | ||
| "pattern": "^\\S+\\.bam$", | ||
| "errorMessage": "BAM file for tumors must be provided'" | ||
| }, | ||
| "tumor_index": { | ||
| "type": "string", | ||
| "pattern": "^\\S+\\.bai$", | ||
| "errorMessage": "BAI file matching to BAM for tumors must be provided'" | ||
| }, | ||
| "control": { | ||
| "errorMessage": "BAM file for as control matching to tumor, if there is", | ||
| "anyOf": [ | ||
| { | ||
| "type": "string", | ||
| "pattern": "^\\S+\\.bam$" | ||
| }, | ||
| { | ||
| "type": "string", | ||
| "maxLength": 0 | ||
| } | ||
| ] | ||
| }, | ||
| "control_index": { | ||
| "errorMessage": "BAI file matching to BAM for as control matching to tumor, if there is", | ||
| "anyOf": [ | ||
| { | ||
| "type": "string", | ||
| "pattern": "^\\S+\\.bai$" | ||
| }, | ||
| { | ||
| "type": "string", | ||
| "maxLength": 0 | ||
| } | ||
| ] | ||
| } | ||
| }, | ||
| "required": ["sample", "tumor", "tumor_index"] | ||
| } | ||
| } |