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6bb4a6a7ee
* Implement PLINK_EXTRACT module * fix plink version number * Update main.nf * Update test_data.config * Update modules/plink/extract/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * just use one channel * fix test with new channel input Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
29 lines
961 B
Text
29 lines
961 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { PLINK_VCF } from '../../../../modules/plink/vcf/main.nf' addParams ( options: [args:'--make-bed --set-missing-var-ids @:#:\\$1:\\$2'])
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include { PLINK_EXTRACT } from '../../../../modules/plink/extract/main.nf' addParams( options: [suffix:'.extract'] )
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workflow test_plink_extract {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_vcf_gz'], checkIfExists: true)
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]
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PLINK_VCF ( input )
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PLINK_VCF.out.bim
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.splitText(file: 'variants.keep', keepHeader: false, by: 10)
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.first()
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.set { ch_variants }
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PLINK_VCF.out.bed
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.concat(PLINK_VCF.out.bim, PLINK_VCF.out.fam.concat(ch_variants))
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.groupTuple()
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.map{ meta, paths -> [meta, paths[0], paths[1], paths[2], paths[3]] }
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.set { ch_extract }
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PLINK_EXTRACT ( ch_extract )
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}
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