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pgx-main from prod added

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Darren Wight
2025-08-18 12:06:58 +02:00
parent fcb0e9aa4c
commit fe48df8676
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#!/usr/bin/env nextflow
nextflow.enable.dsl=1
gene_name = params.gene
up_gene_symbol = gene_name.toUpperCase()
d_base = params.db_init
res_base = params.res_init
caller_base = params.caller_init
output_folder = params.out_dir
params.build='hg38'
if (params.build=='b37') {
db = "${d_base}/${gene_name}/b37"
res_dir = "${res_base}/${gene_name}/res_b37"
caller_dir = "${caller_base}/${gene_name}/b37/bin"
debug37 = "--minimum_extract_score_over_homref=0"
debug38 = ""
if (params.gene=='cyp2d6') {
chrom = "22"
region_a1 = "22:42522000-42542000"
region_a2 = "042522000-042542000"
region_b1 = "22:42522300-42528400"
region_b2 = "042522300-042528400"
} else if (params.gene=='cyp2a6') {
chrom = "19"
region_a1 = "19:41339500-41389490"
region_a2 = "041339500-041389490"
region_b1 = "19:41348500-41358200"
region_b2 = "041348500-041358200"
} else if (params.gene=='cyp2b6') {
chrom = "19"
region_a1 = "19:41487100-41534300"
region_a2 = "041487100-041534300"
region_b1 = "19:41494750-41522800"
region_b2 = "041494750-041522800"
} else if (params.gene=='cyp2c19') {
chrom = "10"
region_a1 = "10:96518000-96613000"
region_a2 = "096518000-096613000"
region_b1 = "10:96519000-96612750"
region_b2 = "096519000-096612750"
} else if (params.gene=='cyp2c9') {
chrom = "10"
region_a1 = "10:96695000-96749500"
region_a2 = "096695000-096749500"
region_b1 = "10:96695750-96748950"
region_b2 = "096695750-096748950"
} else if (params.gene=='cyp2c8') {
chrom = "10"
region_a1 = "10:96786500-96839250"
region_a2 = "096786500-096839250"
region_b1 = "10:96796750-96829600"
region_b2 = "096796750-096829600"
} else if (params.gene=='cyp2e1') {
chrom = "10"
region_a1 = "10:135330300-135352600"
region_a2 = "135330300-135352600"
region_b1 = "10:135339500-135351300"
region_b2 = "135339500-135351300"
} else if (params.gene=='cyp3a4') {
chrom = "7"
region_a1 = "7:99344600-99391800"
region_a2 = "099344600-099391800"
region_b1 = "7:99355450-99382600"
region_b2 = "099355450-099382600"
} else if (params.gene=='cyp3a5') {
chrom = "7"
region_a1 = "7:99235800-99287600"
region_a2 = "099235800-099287600"
region_b1 = "7:99245850-99278250"
region_b2 = "099245850-099278250"
} else if (params.gene=='cyp1a1') {
chrom = "15"
region_a1 = "15:75001900-75027900"
region_a2 = "075001900-075027900"
region_b1 = "15:75011600-75015320"
region_b2 = "075011600-075015320"
} else if (params.gene=='cyp1a2') {
chrom = "15"
region_a1 = "15:75031200-75058900"
region_a2 = "075031200-075058900"
region_b1 = "15:75038200-75047650"
region_b2 = "075038200-075047650"
} else if (params.gene=='cyp4f2') {
chrom = "19"
region_a1 = "19:15978850-16018850"
region_a2 = "015978850-016018850"
region_b1 = "19:15988850-16008850"
region_b2 = "015988850-016008850"
} else if (params.gene=='cypor') {
chrom = "7"
region_a1 = "7:75534473-75626173"
region_a2 = "075534473-075626173"
region_b1 = "7:75549473-75621173"
region_b2 = "075549473-075621173"
}
} else if (params.build=='hg19') {
db = "${d_base}/${gene_name}/b37"
res_dir = "${res_base}/${gene_name}/res_hg19"
caller_dir = "${caller_base}/${gene_name}/b37/bin"
debug37 = "--minimum_extract_score_over_homref=0"
debug38 = ""
if (params.gene=='cyp2d6') {
chrom = "chr22"
region_a1 = "chr22:42522000-42542000"
region_a2 = "042522000-042542000"
region_b1 = "chr22:42522300-42528400"
region_b2 = "042522300-042528400"
} else if (params.gene=='cyp2a6') {
chrom = "chr19"
region_a1 = "chr19:41339500-41389490"
region_a2 = "041339500-041389490"
region_b1 = "chr19:41348500-41358200"
region_b2 = "041348500-041358200"
} else if (params.gene=='cyp2b6') {
chrom = "chr19"
region_a1 = "chr19:41487100-41534300"
region_a2 = "041487100-041534300"
region_b1 = "chr19:41494750-41522800"
region_b2 = "041494750-041522800"
} else if (params.gene=='cyp2c19') {
chrom = "chr10"
region_a1 = "chr10:96518000-96613000"
region_a2 = "096518000-096613000"
region_b1 = "chr10:96519000-96612750"
region_b2 = "096519000-096612750"
} else if (params.gene=='cyp2c9') {
chrom = "chr10"
region_a1 = "chr10:96695000-96749500"
region_a2 = "096695000-096749500"
region_b1 = "chr10:96695750-96748950"
region_b2 = "096695750-096748950"
} else if (params.gene=='cyp2c8') {
chrom = "chr10"
region_a1 = "chr10:96786500-96839250"
region_a2 = "096786500-096839250"
region_b1 = "chr10:96796750-96829600"
region_b2 = "096796750-096829600"
} else if (params.gene=='cyp2e1') {
chrom = "chr10"
region_a1 = "chr10:135330300-135352600"
region_a2 = "135330300-135352600"
region_b1 = "chr10:135339500-135351300"
region_b2 = "135339500-135351300"
} else if (params.gene=='cyp3a4') {
chrom = "chr7"
region_a1 = "chr7:99344600-99391800"
region_a2 = "099344600-099391800"
region_b1 = "chr7:99355450-99382600"
region_b2 = "099355450-099382600"
} else if (params.gene=='cyp3a5') {
chrom = "chr7"
region_a1 = "chr7:99235800-99287600"
region_a2 = "099235800-099287600"
region_b1 = "chr7:99245850-99278250"
region_b2 = "099245850-099278250"
} else if (params.gene=='cyp1a1') {
chrom = "chr15"
region_a1 = "chr15:75001900-75027900"
region_a2 = "075001900-075027900"
region_b1 = "chr15:75011600-75015320"
region_b2 = "075011600-075015320"
} else if (params.gene=='cyp1a2') {
chrom = "chr15"
region_a1 = "chr15:75031200-75058900"
region_a2 = "075031200-075058900"
region_b1 = "chr15:75038200-75047650"
region_b2 = "075038200-075047650"
} else if (params.gene=='cyp4f2') {
chrom = "chr19"
region_a1 = "chr19:15978850-16018850"
region_a2 = "015978850-016018850"
region_b1 = "chr19:15988850-16008850"
region_b2 = "015988850-016008850"
} else if (params.gene=='cypor') {
chrom = "chr7"
region_a1 = "chr7:75534473-75626173"
region_a2 = "075534473-075626173"
region_b1 = "chr7:75549473-75621173"
region_b2 = "075549473-075621173"
}
} else {
db = "${d_base}/${gene_name}/hg38"
res_dir = "${res_base}/${gene_name}/res_hg38"
caller_dir = "${caller_base}/${gene_name}/hg38/bin"
debug37 = ""
debug38 = "--minimum_extract_score_over_homref=0"
if (params.gene=='cyp2d6') {
chrom = "22"
region_a1 = "22:42126000-42137500"
region_a2 = "042126000-042137500"
region_b1 = "22:42126300-42132400"
region_b2 = "042126300-042132400"
transcript = "ENST00000645361"
} else if (params.gene=='cyp2a6') {
chrom = "chr19"
region_a1 = "chr19:40833541-40887450"
region_a2 = "040833541-040887450"
region_b1 = "chr19:40842750-40852250"
region_b2 = "040842750-040852250"
transcript = "ENST00000301141"
} else if (params.gene=='cyp2b6') {
chrom = "chr19"
region_a1 = "chr19:40981280-41028400"
region_a2 = "040981280-041028400"
region_b1 = "chr19:40988800-41016900"
region_b2 = "040988800-041016900"
transcript = "ENST00000324071"
} else if (params.gene=='cyp2c19') {
chrom = "chr10"
region_a1 = "chr10:94752750-94865500"
region_a2 = "094752750-094865500"
region_b1 = "chr10:94759250-94853000"
region_b2 = "094759250-094853000"
transcript = "ENST00000371321"
} else if (params.gene=='cyp2c9') {
chrom = "chr10"
region_a1 = "chr10:94935000-94990000"
region_a2 = "094935000-094990000"
region_b1 = "chr10:94936000-94989200"
region_b2 = "094936000-094989200"
transcript = "ENST00000260682"
} else if (params.gene=='cyp2c8') {
chrom = "chr10"
region_a1 = "chr10:95026750-95079500"
region_a2 = "095026750-095079500"
region_b1 = "chr10:95037050-95069800"
region_b2 = "095037050-095069800"
transcript = "ENST00000371270"
} else if (params.gene=='cyp2e1') {
chrom = "chr10"
region_a1 = "chr10:133517350-133549100"
region_a2 = "133517350-133549100"
region_b1 = "chr10:133522363-133544123"
region_b2 = "133522363-133544123"
transcript = "ENST00000252945"
} else if (params.gene=='cyp3a4') {
chrom = "chr7"
region_a1 = "chr7:99746950-99794100"
region_a2 = "099746950-099794100"
region_b1 = "chr7:99757850-99784950"
region_b2 = "099757850-099784950"
transcript = "ENST00000651514"
} else if (params.gene=='cyp3a5') {
chrom = "chr7"
region_a1 = "chr7:99638200-99690000"
region_a2 = "099638200-099690000"
region_b1 = "chr7:99648250-99680650"
region_b2 = "099648250-099680650"
transcript = "ENST00000222982"
} else if (params.gene=='cyp1a1') {
chrom = "chr15"
region_a1 = "chr15:74709550-74735500"
region_a2 = "074709550-074735500"
region_b1 = "chr15:74719250-74725500"
region_b2 = "074719250-074725500"
transcript = "ENST00000379727"
} else if (params.gene=='cyp1a2') {
chrom = "chr15"
region_a1 = "chr15:74738850-74766600"
region_a2 = "074738850-074766600"
region_b1 = "chr15:74745850-74755280"
region_b2 = "074745850-074755280"
transcript = "ENST00000343932"
} else if (params.gene=='cyp4f2') {
chrom = "chr19"
region_a1 = "chr19:15868100-15908000"
region_a2 = "015868100-015908000"
region_b1 = "chr19:15878000-15898100"
region_b2 = "015878000-015898100"
transcript = "ENST00000221700"
} else if (params.gene=='cypor') {
chrom = "chr7"
region_a1 = "chr7:75905155-75996855"
region_a2 = "075905155-075996855"
region_b1 = "chr7:75910155-75991855"
region_b2 = "075910155-075991855"
transcript = "ENST00000461988"
} else if (params.gene=='nat1') {
chrom = "chr8"
region_a1 = "chr8:18170000-18226000"
region_a2 = "018170000-018226000"
region_b1 = "chr8:18221000-18224000"
region_b2 = "018221000-018224000"
transcript = "ENST00000307719"
} else if (params.gene=='nat2') {
chrom = "chr8"
region_a1 = "chr8:18386000-18402000"
region_a2 = "018386000-018402000"
region_b1 = "chr8:18386000-18402000"
region_b2 = "018386000-018402000"
transcript = "ENST00000286479"
} else if (params.gene=='gstm1') {
chrom = "chr1"
region_a1 = "chr1:109687000-109695000"
region_a2 = "109687000-109695000"
region_b1 = "chr1:109687000-109695000"
region_b2 = "109687000-109695000"
transcript = "ENST00000309851"
} else if (params.gene=='gstt1') {
chrom = "chr22_KI270879v1_alt"
region_a1 = "chr22_KI270879v1_alt:269000-280000"
region_a2 = "000269000-000280000"
region_b1 = "chr22_KI270879v1_alt:269000-280000"
region_b2 = "000269000-000280000"
transcript = "ENST00000612885"
}
}
params.format='binary'
if (params.format=='compressed') {
ext = "cram"
ind = "crai"
cram_options = "--force_use_input_ref_for_cram_reading"
} else {
ext = "bam"
ind = "bai"
cram_options = ""
}
align_file = Channel.fromFilePairs(params.in_bam, type: 'file') { file -> file.name.replaceAll(/.${ext}|.${ind}$/,'') }
align_file.into { data1; data2; data3; data4; data5 }
ref_dir_val = new File("${params.ref_file}").getParent()
ref_genome = new File("${params.ref_file}").getName()
process call_snvs1 {
// maxForks 10
input:
set val(name), file(bam) from data1
path ref_dir from Channel.value("${ref_dir_val}")
path res_dir
output:
set val(name), path("${name}_var_1") into var_ch1
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}/${region_a2}.vcf.gz
"""
}
process call_snvs2 {
// maxForks 10
input:
set val(name), file(bam) from data2
path ref_dir from Channel.value("${ref_dir_val}")
output:
set val(name), path("${name}_var_2") into var_ch2
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}/${region_a2}.vcf.gz
"""
}
process call_sv_del {
// maxForks 10
input:
set val(name), file(bam) from data3
path ref_dir from Channel.value("${ref_dir_val}")
path res_dir
output:
set val(name), path("${name}_sv_del") into sv_ch1
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 ${res_dir}/sv_test.vcf.gz
"""
}
process call_sv_dup {
// maxForks 10
input:
set val(name), file(bam) from data4
path ref_dir from Channel.value("${ref_dir_val}")
path res_dir
output:
set val(name), path("${name}_sv_dup") into sv_ch2
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 ${res_dir}/sv_test3.vcf.gz
"""
}
process get_depth {
// maxForks 10
input:
set val(name), file(bam) from data5
path ref_dir from Channel.value("${ref_dir_val}")
path res_dir
output:
set val(name), file("${name}_${gene_name}_ctrl.depth") into sv_ch3
script:
"""
samtools bedcov --reference ${ref_dir}/${ref_genome} ${res_dir}/test3.bed ${name}.${ext} > ${name}_${gene_name}_ctrl.depth
"""
}
var_ch1.join(var_ch2).set { var_ch_joined }
process format_snvs {
// maxForks 10
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'
input:
set val(name), path("${name}_var_1"), path("${name}_var_2") from var_ch_joined
output:
set val(name), path("${name}_var") into (var_norm1, var_norm2)
set val(name), file("${name}_${gene_name}.vcf.gz"), file("${name}_${gene_name}.vcf.gz.tbi") into var_norm3
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 ${name}_var/${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 -c > ${name}_var/${name}_all_norm.vcf.gz
tabix ${name}_var/${name}_all_norm.vcf.gz
cp ${name}_var/${name}_all_norm.vcf.gz ./${name}_${gene_name}.vcf.gz
cp ${name}_var/${name}_all_norm.vcf.gz.tbi ./${name}_${gene_name}.vcf.gz.tbi
"""
}
process get_core_var {
// maxForks 10
errorStrategy 'ignore'
tag "${name}"
input:
set val(name), path("${name}_vars") from var_norm1
path res_dir
path res_base
path ref_dir from Channel.value("${ref_dir_val}")
path caller_base
output:
set val(name), path("${name}_int") into (core_vars1, core_vars2)
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 -c > ${name}_int/${name}_core.vcf.gz
tabix ${name}_int/${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 -c > ${name}_int/${name}_core.vcf.gz
tabix ${name}_int/${name}_core.vcf.gz
"""
} else {
"""
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"' > ${name}_int/${name}_core_int1.vcf
bcftools csq -p m -v 0 -f ${ref_dir}/${ref_genome} -g ${res_base}/annotation/Homo_sapiens.GRCh38.110.gff3.gz ${name}_int/0000.vcf.gz -o ${name}_int/0000_annot.vcf
python3 ${caller_base}/novel/core_var.py ${name}_int/0000_annot.vcf ${up_gene_symbol} ${transcript} >> ${name}_int/${name}_core_int1.vcf
bcftools sort ${name}_int/${name}_core_int1.vcf -T ${name}_int | bgzip -c > ${name}_int/${name}_core.vcf.gz
tabix ${name}_int/${name}_core.vcf.gz
"""
}
}
process analyse_1 {
// maxForks 10
errorStrategy 'ignore'
tag "${name}"
input:
set val(name), path("${name}_gene_del") from sv_ch1
output:
set val(name), path("${name}_gene_del/${name}_gene_del_summary.txt") into del_ch
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
"""
}
sv_ch2.join(core_vars1).set {dup_int}
process analyse_2 {
// maxForks 10
errorStrategy 'ignore'
tag "${name}"
input:
set val(name), path("${name}_gene_dup"), path("${name}_int") from dup_int
output:
set val(name), path("${name}_gene_dup/${name}_gene_dup_summary.txt") into dup_ch
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
"""
}
var_norm2.join(core_vars2).set {dip_req}
process analyse_3 {
// maxForks 10
errorStrategy 'ignore'
tag "${name}"
input:
set val(name), path("${name}_vars"), path("${name}_int") from dip_req
output:
set val(name), path("${name}_vars/${name}_core_snvs.dip"), path("${name}_vars/${name}_full.dip"), path("${name}_vars/${name}_gt.dip") into prep_ch
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
"""
}
prep_ch.join(del_ch).set {fin_files1}
fin_files1.join(dup_ch).set {fin_files2}
fin_files2.join(sv_ch3).set {fin_files}
process call_stars {
// maxForks 10
publishDir "$output_folder/$gene_name/alleles", mode: 'copy', overwrite: 'true'
errorStrategy 'ignore'
tag "${name}"
input:
set val(name), path("${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/${name}_gene_dup_summary.txt"), file("${name}_${gene_name}_dp") from fin_files
path db
path caller_dir
output:
set val(name), file("${name}_${gene_name}.alleles") into star_ch
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 ${db}/haps_var_new.dbs ${db}/a_scores.dbs > ${name}_${gene_name}.alleles
"""
}