36 lines
958 B
Plaintext
36 lines
958 B
Plaintext
#!/usr/bin/env nextflow
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//haps1 = Channel.fromFilePairs(params.in_pgvcf, type: 'file') { file -> file.name.replaceAll(/.vcf.gz|.tbi$/,'') }
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haps1 = Channel.fromPath(params.in_hap1, type: 'file')
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haps2 = Channel.fromPath(params.in_hap2, type: 'file')
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//haps2 = Channel.fromFilePairs(params.in_haplo, type: 'file') { file -> file.name.replaceAll(/.vcf.gz|.tbi$/,'') }
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haps1
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.combine(haps2)
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.set {data}
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// .println()
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process make_diplo {
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// maxForks 10
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// errorStrategy 'ignore'
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// tag "${name}"
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// label 'big_mem'
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publishDir params.out_dir, mode: 'copy', overwrite: 'true'
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input:
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file(vcfs) from data
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output:
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file("*_diplo.vcf.gz") into diplotypes_ch
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script:
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"""
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tabix ${vcfs.get(0)}
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tabix ${vcfs.get(1)}
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bcftools merge ${vcfs.get(0)} ${vcfs.get(1)} | bgzip -c > ${vcfs.get(0).name.replace(/.vcf.gz/, "")}_${vcfs.get(1).name.replace(/.vcf.gz/, "")}_diplo.vcf.gz
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"""
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} |