843 lines
24 KiB
Plaintext
843 lines
24 KiB
Plaintext
#!/usr/bin/env nextflow
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nextflow.enable.dsl=2
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gene_name = params.gene
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up_gene_symbol = gene_name.toUpperCase()
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d_base = params.db_init
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res_base = params.res_init
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caller_base = params.caller_init
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output_folder = params.out_dir
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params.build='hg38'
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if (params.build=='b37') {
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db = "${d_base}/${gene_name}/b37"
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res_dir = "${res_base}/${gene_name}/res_b37"
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caller_dir = "${caller_base}/${gene_name}/b37/bin"
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debug37 = "--minimum_extract_score_over_homref=0"
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debug38 = ""
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if (params.gene=='cyp2d6') {
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chrom = "22"
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region_a1 = "22:42522000-42542000"
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region_a2 = "042522000-042542000"
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region_b1 = "22:42522300-42528400"
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region_b2 = "042522300-042528400"
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} else if (params.gene=='cyp2a6') {
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chrom = "19"
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region_a1 = "19:41339500-41389490"
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region_a2 = "041339500-041389490"
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region_b1 = "19:41348500-41358200"
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region_b2 = "041348500-041358200"
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} else if (params.gene=='cyp2b6') {
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chrom = "19"
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region_a1 = "19:41487100-41534300"
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region_a2 = "041487100-041534300"
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region_b1 = "19:41494750-41522800"
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region_b2 = "041494750-041522800"
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} else if (params.gene=='cyp2c19') {
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chrom = "10"
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region_a1 = "10:96518000-96613000"
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region_a2 = "096518000-096613000"
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region_b1 = "10:96519000-96612750"
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region_b2 = "096519000-096612750"
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} else if (params.gene=='cyp2c9') {
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chrom = "10"
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region_a1 = "10:96695000-96749500"
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region_a2 = "096695000-096749500"
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region_b1 = "10:96695750-96748950"
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region_b2 = "096695750-096748950"
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} else if (params.gene=='cyp2c8') {
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chrom = "10"
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region_a1 = "10:96786500-96839250"
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region_a2 = "096786500-096839250"
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region_b1 = "10:96796750-96829600"
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region_b2 = "096796750-096829600"
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} else if (params.gene=='cyp2e1') {
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chrom = "10"
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region_a1 = "10:135330300-135352600"
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region_a2 = "135330300-135352600"
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region_b1 = "10:135339500-135351300"
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region_b2 = "135339500-135351300"
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} else if (params.gene=='cyp3a4') {
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chrom = "7"
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region_a1 = "7:99344600-99391800"
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region_a2 = "099344600-099391800"
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region_b1 = "7:99355450-99382600"
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region_b2 = "099355450-099382600"
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} else if (params.gene=='cyp3a5') {
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chrom = "7"
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region_a1 = "7:99235800-99287600"
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region_a2 = "099235800-099287600"
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region_b1 = "7:99245850-99278250"
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region_b2 = "099245850-099278250"
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} else if (params.gene=='cyp1a1') {
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chrom = "15"
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region_a1 = "15:75001900-75027900"
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region_a2 = "075001900-075027900"
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region_b1 = "15:75011600-75015320"
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region_b2 = "075011600-075015320"
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} else if (params.gene=='cyp1a2') {
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chrom = "15"
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region_a1 = "15:75031200-75058900"
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region_a2 = "075031200-075058900"
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region_b1 = "15:75038200-75047650"
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region_b2 = "075038200-075047650"
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} else if (params.gene=='cyp4f2') {
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chrom = "19"
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region_a1 = "19:15978850-16018850"
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region_a2 = "015978850-016018850"
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region_b1 = "19:15988850-16008850"
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region_b2 = "015988850-016008850"
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} else if (params.gene=='cypor') {
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chrom = "7"
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region_a1 = "7:75534473-75626173"
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region_a2 = "075534473-075626173"
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region_b1 = "7:75549473-75621173"
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region_b2 = "075549473-075621173"
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}
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} else if (params.build=='hg19') {
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db = "${d_base}/${gene_name}/b37"
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res_dir = "${res_base}/${gene_name}/res_hg19"
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caller_dir = "${caller_base}/${gene_name}/b37/bin"
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debug37 = "--minimum_extract_score_over_homref=0"
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debug38 = ""
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if (params.gene=='cyp2d6') {
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chrom = "chr22"
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region_a1 = "chr22:42522000-42542000"
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region_a2 = "042522000-042542000"
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region_b1 = "chr22:42522300-42528400"
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region_b2 = "042522300-042528400"
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} else if (params.gene=='cyp2a6') {
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chrom = "chr19"
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region_a1 = "chr19:41339500-41389490"
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region_a2 = "041339500-041389490"
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region_b1 = "chr19:41348500-41358200"
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region_b2 = "041348500-041358200"
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} else if (params.gene=='cyp2b6') {
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chrom = "chr19"
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region_a1 = "chr19:41487100-41534300"
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region_a2 = "041487100-041534300"
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region_b1 = "chr19:41494750-41522800"
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region_b2 = "041494750-041522800"
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} else if (params.gene=='cyp2c19') {
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chrom = "chr10"
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region_a1 = "chr10:96518000-96613000"
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region_a2 = "096518000-096613000"
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region_b1 = "chr10:96519000-96612750"
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region_b2 = "096519000-096612750"
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} else if (params.gene=='cyp2c9') {
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chrom = "chr10"
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region_a1 = "chr10:96695000-96749500"
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region_a2 = "096695000-096749500"
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region_b1 = "chr10:96695750-96748950"
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region_b2 = "096695750-096748950"
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} else if (params.gene=='cyp2c8') {
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chrom = "chr10"
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region_a1 = "chr10:96786500-96839250"
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region_a2 = "096786500-096839250"
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region_b1 = "chr10:96796750-96829600"
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region_b2 = "096796750-096829600"
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} else if (params.gene=='cyp2e1') {
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chrom = "chr10"
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region_a1 = "chr10:135330300-135352600"
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region_a2 = "135330300-135352600"
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region_b1 = "chr10:135339500-135351300"
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region_b2 = "135339500-135351300"
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} else if (params.gene=='cyp3a4') {
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chrom = "chr7"
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region_a1 = "chr7:99344600-99391800"
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region_a2 = "099344600-099391800"
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region_b1 = "chr7:99355450-99382600"
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region_b2 = "099355450-099382600"
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} else if (params.gene=='cyp3a5') {
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chrom = "chr7"
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region_a1 = "chr7:99235800-99287600"
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region_a2 = "099235800-099287600"
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region_b1 = "chr7:99245850-99278250"
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region_b2 = "099245850-099278250"
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} else if (params.gene=='cyp1a1') {
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chrom = "chr15"
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region_a1 = "chr15:75001900-75027900"
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region_a2 = "075001900-075027900"
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region_b1 = "chr15:75011600-75015320"
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region_b2 = "075011600-075015320"
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} else if (params.gene=='cyp1a2') {
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chrom = "chr15"
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region_a1 = "chr15:75031200-75058900"
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region_a2 = "075031200-075058900"
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region_b1 = "chr15:75038200-75047650"
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region_b2 = "075038200-075047650"
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} else if (params.gene=='cyp4f2') {
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chrom = "chr19"
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region_a1 = "chr19:15978850-16018850"
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region_a2 = "015978850-016018850"
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region_b1 = "chr19:15988850-16008850"
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region_b2 = "015988850-016008850"
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} else if (params.gene=='cypor') {
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chrom = "chr7"
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region_a1 = "chr7:75534473-75626173"
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region_a2 = "075534473-075626173"
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region_b1 = "chr7:75549473-75621173"
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region_b2 = "075549473-075621173"
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}
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} else {
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db = "${d_base}/${gene_name}/hg38"
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res_dir = "${res_base}/${gene_name}/res_hg38"
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caller_dir = "${caller_base}/${gene_name}/hg38/bin"
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debug37 = ""
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debug38 = "--minimum_extract_score_over_homref=0"
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if (params.gene=='cyp2d6') {
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chrom = "chr22"
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region_a1 = "chr22:42126000-42137500"
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region_a2 = "042126000-042137500"
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region_b1 = "chr22:42126300-42132400"
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region_b2 = "042126300-042132400"
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transcript = "ENST00000645361"
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} else if (params.gene=='cyp2a6') {
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chrom = "chr19"
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region_a1 = "chr19:40833541-40887450"
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region_a2 = "040833541-040887450"
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region_b1 = "chr19:40842750-40852250"
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region_b2 = "040842750-040852250"
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transcript = "ENST00000301141"
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} else if (params.gene=='cyp2b6') {
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chrom = "chr19"
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region_a1 = "chr19:40981280-41028400"
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region_a2 = "040981280-041028400"
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region_b1 = "chr19:40988800-41016900"
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region_b2 = "040988800-041016900"
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transcript = "ENST00000324071"
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} else if (params.gene=='cyp2c19') {
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chrom = "chr10"
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region_a1 = "chr10:94752750-94865500"
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region_a2 = "094752750-094865500"
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region_b1 = "chr10:94759250-94853000"
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region_b2 = "094759250-094853000"
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transcript = "ENST00000371321"
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} else if (params.gene=='cyp2c9') {
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chrom = "chr10"
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region_a1 = "chr10:94935000-94990000"
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region_a2 = "094935000-094990000"
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region_b1 = "chr10:94936000-94989200"
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region_b2 = "094936000-094989200"
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transcript = "ENST00000260682"
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} else if (params.gene=='cyp2c8') {
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chrom = "chr10"
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region_a1 = "chr10:95026750-95079500"
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region_a2 = "095026750-095079500"
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region_b1 = "chr10:95037050-95069800"
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region_b2 = "095037050-095069800"
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transcript = "ENST00000371270"
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} else if (params.gene=='cyp2e1') {
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chrom = "chr10"
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region_a1 = "chr10:133517350-133549100"
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region_a2 = "133517350-133549100"
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region_b1 = "chr10:133522363-133544123"
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region_b2 = "133522363-133544123"
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transcript = "ENST00000252945"
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} else if (params.gene=='cyp3a4') {
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chrom = "chr7"
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region_a1 = "chr7:99746950-99794100"
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region_a2 = "099746950-099794100"
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region_b1 = "chr7:99757850-99784950"
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region_b2 = "099757850-099784950"
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transcript = "ENST00000651514"
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} else if (params.gene=='cyp3a5') {
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chrom = "chr7"
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region_a1 = "chr7:99638200-99690000"
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region_a2 = "099638200-099690000"
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region_b1 = "chr7:99648250-99680650"
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region_b2 = "099648250-099680650"
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transcript = "ENST00000222982"
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} else if (params.gene=='cyp1a1') {
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chrom = "chr15"
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region_a1 = "chr15:74709550-74735500"
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region_a2 = "074709550-074735500"
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region_b1 = "chr15:74719250-74725500"
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region_b2 = "074719250-074725500"
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transcript = "ENST00000379727"
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} else if (params.gene=='cyp1a2') {
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chrom = "chr15"
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region_a1 = "chr15:74738850-74766600"
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region_a2 = "074738850-074766600"
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region_b1 = "chr15:74745850-74755280"
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region_b2 = "074745850-074755280"
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transcript = "ENST00000343932"
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} else if (params.gene=='cyp4f2') {
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chrom = "chr19"
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region_a1 = "chr19:15868100-15908000"
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region_a2 = "015868100-015908000"
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region_b1 = "chr19:15878000-15898100"
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region_b2 = "015878000-015898100"
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transcript = "ENST00000221700"
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} else if (params.gene=='cypor') {
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chrom = "chr7"
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region_a1 = "chr7:75905155-75996855"
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region_a2 = "075905155-075996855"
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region_b1 = "chr7:75910155-75991855"
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region_b2 = "075910155-075991855"
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transcript = "ENST00000461988"
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} else if (params.gene=='nat1') {
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chrom = "chr8"
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region_a1 = "chr8:18170000-18226000"
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region_a2 = "018170000-018226000"
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region_b1 = "chr8:18221000-18224000"
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region_b2 = "018221000-018224000"
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transcript = "ENST00000307719"
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} else if (params.gene=='nat2') {
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chrom = "chr8"
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region_a1 = "chr8:18386000-18402000"
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region_a2 = "018386000-018402000"
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region_b1 = "chr8:18386000-18402000"
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region_b2 = "018386000-018402000"
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transcript = "ENST00000286479"
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} else if (params.gene=='gstm1') {
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chrom = "chr1"
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region_a1 = "chr1:109687000-109695000"
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region_a2 = "109687000-109695000"
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region_b1 = "chr1:109687000-109695000"
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region_b2 = "109687000-109695000"
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transcript = "ENST00000309851"
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} else if (params.gene=='gstt1') {
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chrom = "chr22_KI270879v1_alt"
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region_a1 = "chr22_KI270879v1_alt:269000-280000"
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region_a2 = "000269000-000280000"
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region_b1 = "chr22_KI270879v1_alt:269000-280000"
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region_b2 = "000269000-000280000"
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transcript = "ENST00000612885"
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} else if (params.gene=='slco1b1') {
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chrom = "chr12"
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region_a1 = "chr12:21120000-21250000"
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region_a2 = "021120000-021250000"
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region_b1 = "chr12:21120000-21250000"
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region_b2 = "021120000-021250000"
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transcript = "ENST00000256958"
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} else if (params.gene=='nudt15') {
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chrom = "chr13"
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region_a1 = "chr13:48037500-48055000"
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region_a2 = "048037500-048055000"
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region_b1 = "chr13:48037500-48055000"
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region_b2 = "048037500-048055000"
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transcript = "ENST00000258662"
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} else if (params.gene=='tpmt') {
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chrom = "chr6"
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region_a1 = "chr6:18128000-18155500"
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region_a2 = "018128000-018155500"
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region_b1 = "chr6:18128500-18155000"
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region_b2 = "018128500-018155000"
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transcript = "ENST00000309983"
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} else if (params.gene=='ugt1a1') {
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chrom = "chr2"
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region_a1 = "chr2:233758500-233772600"
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region_a2 = "233758500-233772600"
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region_b1 = "chr2:233759000-233772000"
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region_b2 = "233759000-233772000"
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transcript = "ENST00000305208"
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}
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}
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params.format='binary'
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if (params.format=='compressed') {
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ext = "cram"
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ind = "crai"
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cram_options = "--force_use_input_ref_for_cram_reading"
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} else {
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ext = "bam"
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ind = "bai"
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cram_options = ""
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}
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// align_file = Channel.fromFilePairs(params.in_bam, type: 'file') { file -> file.name.replaceAll(/.${ext}|.${ind}$/,'') }
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// align_file.into { data1; data2; data3; data4; data5 }
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ref_dir_val = new File("${params.ref_file}").getParent()
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ref_genome = new File("${params.ref_file}").getName()
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workflow {
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ref_ch = Channel.value("${ref_dir_val}")
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data_ch = Channel.fromFilePairs(params.in_bam, type: 'file') { file -> file.name.replaceAll(/.${ext}|.${ind}$/,'') }
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call_snvs1(data_ch, ref_ch, res_dir)
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call_snvs2(data_ch, ref_ch)
|
|
call_sv_del(data_ch, ref_ch, res_dir)
|
|
call_sv_dup(data_ch, ref_ch, res_dir)
|
|
get_depth(data_ch, ref_ch, res_dir)
|
|
call_snvs1.out.join(call_snvs2.out).set {var_ch_joined}
|
|
format_snvs(var_ch_joined)
|
|
save_vcfs(format_snvs.out)
|
|
get_core_var(format_snvs.out, res_dir, res_base, ref_ch, caller_base)
|
|
get_core_var.out.join(data_ch).set {phase_ch}
|
|
phase_snvs(phase_ch, ref_ch)
|
|
analyse_1(call_sv_del.out)
|
|
call_sv_dup.out.join(get_core_var.out).set {dup_int}
|
|
analyse_2(dup_int)
|
|
format_snvs.out.join(get_core_var.out).set {dip_req}
|
|
analyse_3(dip_req)
|
|
analyse_4(phase_snvs.out)
|
|
analyse_3.out.join(analyse_1.out).set {fin_files1}
|
|
fin_files1.join(analyse_2.out).set {fin_files2}
|
|
fin_files2.join(get_depth.out).set {fin_files3}
|
|
fin_files3.join(analyse_4.out).set {fin_files}
|
|
call_stars(fin_files, db, caller_dir)
|
|
}
|
|
|
|
|
|
process call_snvs1 {
|
|
// maxForks 10
|
|
|
|
input:
|
|
tuple val(name), path(bam)
|
|
path ref_dir
|
|
path res_dir
|
|
|
|
output:
|
|
tuple val(name), path("${name}_var_1")
|
|
|
|
script:
|
|
ext1 = bam[0].getExtension()
|
|
if (ext1=='bam')
|
|
sam_ind='bam.bai'
|
|
|
|
else if (ext1=='cram')
|
|
sam_ind='cram.crai'
|
|
|
|
else if (ext1=='crai')
|
|
sam_ind='crai'
|
|
|
|
else
|
|
sam_ind='bai'
|
|
|
|
"""
|
|
graphtyper genotype ${ref_dir}/${ref_genome} --sam=${name}.${ext} --sams_index=<(echo ${name}.${sam_ind}) --region=${region_a1} --output=${name}_var_1 --prior_vcf=${res_dir}/common_plus_core_var.vcf.gz -a ${debug38} ${cram_options}
|
|
bcftools concat ${name}_var_1/${chrom}/*.vcf.gz > ${name}_var_1/${chrom}/${region_a2}.vcf
|
|
bgzip -f ${name}_var_1/${chrom}/${region_a2}.vcf
|
|
tabix -f ${name}_var_1/${chrom}/${region_a2}.vcf.gz
|
|
|
|
"""
|
|
|
|
}
|
|
|
|
|
|
process call_snvs2 {
|
|
// maxForks 10
|
|
|
|
input:
|
|
tuple val(name), path(bam)
|
|
path ref_dir
|
|
|
|
output:
|
|
tuple val(name), path("${name}_var_2")
|
|
|
|
script:
|
|
ext1 = bam[0].getExtension()
|
|
if (ext1=='bam')
|
|
sam_ind='bam.bai'
|
|
|
|
else if (ext1=='cram')
|
|
sam_ind='cram.crai'
|
|
|
|
else if (ext1=='crai')
|
|
sam_ind='crai'
|
|
|
|
else
|
|
sam_ind='bai'
|
|
|
|
"""
|
|
graphtyper genotype ${ref_dir}/${ref_genome} --sam=${name}.${ext} --sams_index=<(echo ${name}.${sam_ind}) --region=${region_a1} --output=${name}_var_2 -a ${debug38} ${debug37} ${cram_options}
|
|
bcftools concat ${name}_var_2/${chrom}/*.vcf.gz > ${name}_var_2/${chrom}/${region_a2}.vcf
|
|
bgzip -f ${name}_var_2/${chrom}/${region_a2}.vcf
|
|
tabix -f ${name}_var_2/${chrom}/${region_a2}.vcf.gz
|
|
|
|
"""
|
|
|
|
}
|
|
|
|
|
|
process call_sv_del {
|
|
// maxForks 10
|
|
|
|
input:
|
|
tuple val(name), path(bam)
|
|
path ref_dir
|
|
path res_dir
|
|
|
|
output:
|
|
tuple val(name), path("${name}_sv_del")
|
|
|
|
script:
|
|
ext1 = bam[0].getExtension()
|
|
if (ext1=='bam')
|
|
sam_ind='bam.bai'
|
|
|
|
else if (ext1=='cram')
|
|
sam_ind='cram.crai'
|
|
|
|
else if (ext1=='crai')
|
|
sam_ind='crai'
|
|
|
|
else
|
|
sam_ind='bai'
|
|
|
|
"""
|
|
graphtyper genotype_sv ${ref_dir}/${ref_genome} --sam=${name}.${ext} --region=${region_a1} --output=${name}_sv_del ${res_dir}/sv_test.vcf.gz
|
|
|
|
"""
|
|
|
|
}
|
|
|
|
process call_sv_dup {
|
|
// maxForks 10
|
|
|
|
input:
|
|
tuple val(name), path(bam)
|
|
path ref_dir
|
|
path res_dir
|
|
|
|
output:
|
|
tuple val(name), path("${name}_sv_dup")
|
|
|
|
script:
|
|
ext1 = bam[0].getExtension()
|
|
if (ext1=='bam')
|
|
sam_ind='bam.bai'
|
|
|
|
else if (ext1=='cram')
|
|
sam_ind='cram.crai'
|
|
|
|
else if (ext1=='crai')
|
|
sam_ind='crai'
|
|
|
|
else
|
|
sam_ind='bai'
|
|
|
|
"""
|
|
graphtyper genotype_sv ${ref_dir}/${ref_genome} --sam=${name}.${ext} --region=${region_a1} --output=${name}_sv_dup ${res_dir}/sv_test3.vcf.gz
|
|
|
|
"""
|
|
}
|
|
|
|
|
|
process get_depth {
|
|
// maxForks 10
|
|
|
|
input:
|
|
tuple val(name), path(bam)
|
|
path ref_dir
|
|
path res_dir
|
|
|
|
output:
|
|
tuple val(name), path("${name}_${gene_name}_ctrl.depth")
|
|
|
|
script:
|
|
|
|
"""
|
|
samtools bedcov --reference ${ref_dir}/${ref_genome} ${res_dir}/test3.bed ${name}.${ext} > ${name}_${gene_name}_ctrl.depth
|
|
|
|
"""
|
|
|
|
}
|
|
|
|
|
|
process format_snvs {
|
|
// maxForks 10
|
|
|
|
// publishDir "$output_folder/$gene_name/variants", mode: 'copy', overwrite: 'true', saveAs: { ${name}_var/${name}_all_norm.vcf.gz -> "${name}_${gene_name}.vcf.gz" }
|
|
|
|
input:
|
|
tuple val(name), path("${name}_var_1"), path("${name}_var_2")
|
|
|
|
output:
|
|
tuple val(name), path("*")
|
|
|
|
script:
|
|
|
|
"""
|
|
bcftools isec -p ${name}_var -Oz ${name}_var_1/${chrom}/${region_a2}.vcf.gz ${name}_var_2/${chrom}/${region_a2}.vcf.gz
|
|
bcftools concat -a -D -r ${region_b1} ${name}_var/0000.vcf.gz ${name}_var/0001.vcf.gz ${name}_var/0002.vcf.gz -Oz -o ${name}_var/${name}_${region_b2}.vcf.gz
|
|
tabix -f ${name}_var/${name}_${region_b2}.vcf.gz
|
|
bcftools norm -m - ${name}_var/${name}_${region_b2}.vcf.gz | bcftools view -e 'GT="1/0"' | bcftools view -e 'GT="0/0"' | bcftools view -e 'FILTER="PASS" & INFO/QD<10 || 0<ABHet<0.25' | bgzip -cf > ${name}_var/${name}_all_norm.vcf.gz
|
|
tabix -f ${name}_var/${name}_all_norm.vcf.gz
|
|
|
|
"""
|
|
|
|
}
|
|
|
|
|
|
process save_vcfs {
|
|
|
|
publishDir "$output_folder/$gene_name/variants", pattern: '*vcf.gz', mode: 'copy', overwrite: 'true'
|
|
publishDir "$output_folder/$gene_name/variants", pattern: '*vcf.gz.tbi', mode: 'copy', overwrite: 'true'
|
|
|
|
errorStrategy 'ignore'
|
|
tag "${name}"
|
|
|
|
input:
|
|
tuple val(name), path("${name}_vars")
|
|
|
|
output:
|
|
tuple val(name), path("*")
|
|
|
|
script:
|
|
"""
|
|
cp ${name}_vars/${name}_all_norm.vcf.gz ./${name}_${gene_name}.vcf.gz
|
|
cp ${name}_vars/${name}_all_norm.vcf.gz.tbi ./${name}_${gene_name}.vcf.gz.tbi
|
|
"""
|
|
|
|
}
|
|
|
|
process get_core_var {
|
|
// maxForks 10
|
|
|
|
errorStrategy 'ignore'
|
|
tag "${name}"
|
|
|
|
input:
|
|
tuple val(name), path("${name}_vars")
|
|
path res_dir
|
|
path res_base
|
|
path ref_dir
|
|
path caller_base
|
|
|
|
output:
|
|
tuple val(name), path("${name}_int")
|
|
|
|
script:
|
|
|
|
if (params.build=='b37') {
|
|
|
|
"""
|
|
bcftools isec ${name}_vars/${name}_all_norm.vcf.gz ${res_dir}/allele_def_var.vcf.gz -p ${name}_int -Oz
|
|
bcftools norm -m - ${name}_int/0002.vcf.gz | bcftools view -e 'GT="1/0"' | bcftools view -e 'GT="0/0"' | bgzip -cf > ${name}_int/${name}_core.vcf.gz
|
|
tabix -f ${name}_int/${name}_core.vcf.gz
|
|
"""
|
|
|
|
} else if (params.build=='hg19') {
|
|
|
|
"""
|
|
bcftools isec ${name}_vars/${name}_all_norm.vcf.gz ${res_dir}/allele_def_var.vcf.gz -p ${name}_int -Oz
|
|
bcftools norm -m - ${name}_int/0002.vcf.gz | bcftools view -e 'GT="1/0"' | bcftools view -e 'GT="0/0"' | bgzip -cf > ${name}_int/${name}_core.vcf.gz
|
|
tabix -f ${name}_int/${name}_core.vcf.gz
|
|
"""
|
|
|
|
} else {
|
|
|
|
"""
|
|
bcftools csq -p m -v 0 -f ${ref_dir}/${ref_genome} -g ${res_base}/annotation/Homo_sapiens.GRCh38.110.gff3.gz ${name}_vars/${name}_all_norm.vcf.gz -o ${name}_vars/${name}_all_norm_annot.vcf
|
|
bgzip ${name}_vars/${name}_all_norm_annot.vcf
|
|
tabix -f ${name}_vars/${name}_all_norm_annot.vcf.gz
|
|
|
|
bcftools isec ${name}_vars/${name}_all_norm_annot.vcf.gz ${res_dir}/allele_def_var.vcf.gz -p ${name}_int -Oz
|
|
bcftools norm -m - ${name}_int/0002.vcf.gz | bcftools view -e 'GT="1/0"' | bcftools view -e 'GT="0/0"' > ${name}_int/${name}_core_int1.vcf
|
|
|
|
bgzip -d ${name}_int/0000.vcf.gz
|
|
python3 ${caller_base}/novel/core_var.py ${name}_int/0000.vcf ${up_gene_symbol} ${transcript} >> ${name}_int/${name}_core_int1.vcf
|
|
bcftools sort ${name}_int/${name}_core_int1.vcf -T ${name}_int | bgzip -cf > ${name}_int/${name}_core.vcf.gz
|
|
tabix -f ${name}_int/${name}_core.vcf.gz
|
|
|
|
"""
|
|
}
|
|
}
|
|
|
|
|
|
process phase_snvs {
|
|
label 'phase'
|
|
|
|
errorStrategy 'ignore'
|
|
tag "${name}"
|
|
|
|
// publishDir "$output_folder/phased_vcfs", mode: 'copy', overwrite: 'true'
|
|
|
|
input:
|
|
tuple val(name), path("${name}_int1"), path(bam)
|
|
path ref_dir
|
|
|
|
output:
|
|
tuple val(name), path("${name}_${gene_name}_phased.vcf.gz")
|
|
|
|
script:
|
|
|
|
"""
|
|
whatshap phase --output ${name}_${gene_name}_phased.vcf.gz --reference ${ref_dir}/${ref_genome} --chromosome $chrom ${name}_int1/${name}_core.vcf.gz ${name}.${ext} --indels
|
|
|
|
"""
|
|
}
|
|
|
|
process analyse_1 {
|
|
// maxForks 10
|
|
|
|
errorStrategy 'ignore'
|
|
tag "${name}"
|
|
|
|
input:
|
|
tuple val(name), path("${name}_gene_del")
|
|
|
|
output:
|
|
tuple val(name), path("${name}_gene_del/${name}_gene_del_summary.txt")
|
|
|
|
script:
|
|
|
|
"""
|
|
bcftools query -f'%ID\t%ALT\t[%GT\t%DP]\t%INFO/ABHet\t%INFO/ABHom\n' ${name}_gene_del/${chrom}/${region_a2}.vcf.gz > ${name}_gene_del/${name}_gene_del_summary.txt
|
|
"""
|
|
|
|
}
|
|
|
|
|
|
process analyse_2 {
|
|
// maxForks 10
|
|
|
|
errorStrategy 'ignore'
|
|
tag "${name}"
|
|
|
|
input:
|
|
tuple val(name), path("${name}_gene_dup"), path("${name}_int")
|
|
|
|
output:
|
|
tuple val(name), path("${name}_gene_dup/${name}_gene_dup_summary.txt")
|
|
|
|
script:
|
|
|
|
"""
|
|
bcftools query -f'%POS~%REF>%ALT\t[%GT\t%DP]\t%INFO/ABHet\t%INFO/ABHom\n' -i'GT="alt"' ${name}_gene_dup/${chrom}/${region_a2}.vcf.gz > ${name}_gene_dup/${name}_gene_dup_summary.txt
|
|
bcftools query -f'%POS~%REF>%ALT\t[%GT\t%DP]\t%INFO/ABHet\t%INFO/ABHom\n' -i'GT="alt"' ${name}_int/${name}_core.vcf.gz >> ${name}_gene_dup/${name}_gene_dup_summary.txt
|
|
|
|
"""
|
|
|
|
}
|
|
|
|
|
|
process analyse_3 {
|
|
// maxForks 10
|
|
|
|
errorStrategy 'ignore'
|
|
tag "${name}"
|
|
|
|
input:
|
|
tuple val(name), path("${name}_vars"), path("${name}_int")
|
|
|
|
output:
|
|
tuple val(name), path("${name}_vars/${name}_core_snvs.dip"), path("${name}_vars/${name}_full.dip"), path("${name}_vars/${name}_gt.dip")
|
|
|
|
script:
|
|
"""
|
|
bcftools query -f'[%POS~%REF>%ALT~%GT\n]' ${name}_int/${name}_core.vcf.gz > ${name}_vars/${name}_core_snvs.dip
|
|
bcftools query -f '%POS~%REF>%ALT\n' ${name}_vars/${name}_all_norm.vcf.gz > ${name}_vars/${name}_full.dip
|
|
bcftools query -f'[%POS~%REF>%ALT~%GT\n]' ${name}_vars/${name}_all_norm.vcf.gz > ${name}_vars/${name}_gt.dip
|
|
|
|
"""
|
|
|
|
}
|
|
|
|
|
|
process analyse_4 {
|
|
|
|
errorStrategy 'ignore'
|
|
tag "${name}"
|
|
|
|
input:
|
|
tuple val(name), path(phased_vcf)
|
|
|
|
output:
|
|
tuple val(name), path("${name}_${gene_name}_hap_snvs.dip")
|
|
|
|
script:
|
|
"""
|
|
tabix -f ${phased_vcf}
|
|
bcftools query -e 'GT="0|1" || GT="0/1"' -f'[%POS~%REF>%ALT;]' ${phased_vcf} | rev | cut -d";" -f2- | rev > ${name}_${gene_name}_hap_snvs.dip
|
|
bcftools query -e 'GT="1|0" || GT="0/1"' -f'[%POS~%REF>%ALT;]' ${phased_vcf} | rev | cut -d";" -f2- | rev >> ${name}_${gene_name}_hap_snvs.dip
|
|
"""
|
|
|
|
}
|
|
|
|
|
|
process call_stars {
|
|
// maxForks 10
|
|
|
|
publishDir "$output_folder/$gene_name/alleles", mode: 'copy', overwrite: 'true'
|
|
|
|
errorStrategy 'ignore'
|
|
tag "${name}"
|
|
|
|
input:
|
|
tuple val(name), path("${name}_vars/${name}_core_snvs.dip"), path("${name}_vars/${name}_full.dip"), path("${name}_vars/${name}_gt.dip"), path("${name}_gene_del/${name}_gene_del_summary.txt"), path("${name}_gene_dup/${name}_gene_dup_summary.txt"), path("${name}_${gene_name}_dp"), path("${name}_${gene_name}_hap_snvs.dip")
|
|
path db
|
|
path caller_dir
|
|
|
|
output:
|
|
tuple val(name), path("${name}_${gene_name}.alleles")
|
|
|
|
script:
|
|
|
|
"""
|
|
python3 ${caller_dir}/stellarpgx.py ${db}/diplo_db_debugged2.dbs ${name}_vars/${name}_core_snvs.dip ${name}_vars/${name}_full.dip ${name}_vars/${name}_gt.dip ${db}/genotypes4.dbs ${name}_gene_del/${name}_gene_del_summary.txt ${name}_gene_dup/${name}_gene_dup_summary.txt ${name}_${gene_name}_dp ${name}_${gene_name}_hap_snvs.dip ${db}/haps_var_new.dbs ${db}/a_scores.dbs > ${name}_${gene_name}.alleles
|
|
|
|
"""
|
|
|
|
}
|
|
|