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FEAT: add CNVKIT + base skeleton #5
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Some pointers, but overall LGTM :)
"anyOf": [ | ||
{ | ||
"type": "string", | ||
"pattern": "^\\S+\\.bam$" | ||
}, | ||
{ | ||
"type": "string", | ||
"maxLength": 0 | ||
} | ||
], |
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"anyOf": [ | |
{ | |
"type": "string", | |
"pattern": "^\\S+\\.bam$" | |
}, | |
{ | |
"type": "string", | |
"maxLength": 0 | |
} | |
], | |
"type": "string", | |
"pattern": "^\\S+\\.bam$", |
You don't need to specify empty fields in the schema, nf-validation
automatically skips validation of empty fields, if they are not required :). And I think anyOf
doesn't work for the conversion to a channel (I've not tested it though).
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I copy paste code from another PR, if it's ok with you, I'd rather fix this part in a dedicated PR
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Yeah that's okay! :)
"anyOf": [ | ||
{ | ||
"type": "string", | ||
"format": "file-path", | ||
"exists": true, | ||
"mimetype": "text/csv", | ||
"pattern": "^\\S+\\.csv$" | ||
}, | ||
{ | ||
"type": "string", | ||
"maxLength": 0 | ||
} |
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Same here :)
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same here ;-)
) | ||
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
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Allright fine by me :)
Close #3