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e687c7025a
* add plink2_extract * fix test yml path * Update modules/plink2/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/plink2/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * compress output * add DOI * make outputs less ambiguous * update test for compressed output * brain is dumb * Update modules/plink2/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
30 lines
869 B
Text
30 lines
869 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { PLINK2_VCF } from '../../../../modules/plink2/vcf/main.nf'
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include { PLINK2_EXTRACT } from '../../../../modules/plink2/extract/main.nf'
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workflow test_plink2_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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PLINK2_VCF ( input )
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PLINK2_VCF.out.pvar
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.splitText(file: 'variants.keep', keepHeader: false, by: 10)
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.last()
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.set { ch_variants }
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ch_variants.view()
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PLINK2_VCF.out.pgen
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.concat(PLINK2_VCF.out.psam, PLINK2_VCF.out.pvar.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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PLINK2_EXTRACT ( ch_extract )
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}
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