FEAT: add CNVKIT + base skeleton #5
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nvnieuwk
reviewed
Jul 10, 2023
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| "anyOf": [ | ||
| { | ||
| "type": "string", | ||
| "pattern": "^\\S+\\.bam$" | ||
| }, | ||
| { | ||
| "type": "string", | ||
| "maxLength": 0 | ||
| } | ||
| ], |
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Suggested change
| "anyOf": [ | |
| { | |
| "type": "string", | |
| "pattern": "^\\S+\\.bam$" | |
| }, | |
| { | |
| "type": "string", | |
| "maxLength": 0 | |
| } | |
| ], | |
| "type": "string", | |
| "pattern": "^\\S+\\.bam$", |
You don't need to specify empty fields in the schema, nf-validation automatically skips validation of empty fields, if they are not required :). And I think anyOf doesn't work for the conversion to a channel (I've not tested it though).
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I copy paste code from another PR, if it's ok with you, I'd rather fix this part in a dedicated PR
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| "anyOf": [ | ||
| { | ||
| "type": "string", | ||
| "format": "file-path", | ||
| "exists": true, | ||
| "mimetype": "text/csv", | ||
| "pattern": "^\\S+\\.csv$" | ||
| }, | ||
| { | ||
| "type": "string", | ||
| "maxLength": 0 | ||
| } |
| ) | ||
| ch_versions = ch_versions.mix(FASTQC.out.versions.first()) | ||
| if (params.tools && params.tools.split(',').contains('cnvkit')) { | ||
| CNVKIT_BATCH ( ch_input.bam.map{meta, bam -> [ meta, [], bam ]}, ch_fasta, [], [], [], true ) |
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Why don't you also convert the CRAM files to BAM and add them here?
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Let's do that in a separate PR.
I'd love to have the basic skeleton included that way I can add more tools and work on more features separately
nvnieuwk
approved these changes
Jul 10, 2023
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