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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,38 +1,38 @@ | ||
| include { BCFTOOLS_MPILEUP } from '../../../modules/nf-core/bcftools/mpileup/main.nf' | ||
| include { BCFTOOLS_INDEX } from '../../../modules/nf-core/bcftools/index/main.nf' | ||
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| workflow COMPUTE_GL { | ||
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| take: | ||
| ch_input // channel: [ [id, ref], bam, bai ] | ||
| ch_target // channel: [ [panel], sites, tsv] | ||
| ch_fasta // channel: [ [ref], fasta, fai] | ||
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| main: | ||
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| ch_versions = Channel.empty() | ||
| ch_multiqc_files = Channel.empty() | ||
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| ch_mpileup = ch_input | ||
| .combine(ch_target) | ||
| .map{metaI, bam, bai, metaP, sites, tsv -> | ||
| [metaI + metaP, bam, sites, tsv]} | ||
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| BCFTOOLS_MPILEUP( | ||
| ch_mpileup, | ||
| ch_fasta, | ||
| false | ||
| ) | ||
| ch_versions = ch_versions.mix(BCFTOOLS_MPILEUP.out.versions.first()) | ||
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| ch_output = BCFTOOLS_MPILEUP.out.vcf | ||
| .combine(BCFTOOLS_MPILEUP.out.tbi, by:0) | ||
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| ch_multiqc_files = ch_multiqc_files.mix(BCFTOOLS_MPILEUP.out.stats.map{ it[1] }) | ||
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| emit: | ||
| vcf = ch_output // channel: [ [id, panel], vcf, tbi ] | ||
| versions = ch_versions // channel: [ versions.yml ] | ||
| multiqc_files = ch_multiqc_files | ||
| } | ||
| include { BCFTOOLS_MPILEUP } from '../../../modules/nf-core/bcftools/mpileup/main.nf' | ||
| include { BCFTOOLS_INDEX } from '../../../modules/nf-core/bcftools/index/main.nf' | ||
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| workflow COMPUTE_GL { | ||
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| take: | ||
| ch_input // channel: [ [id, ref], bam, bai ] | ||
| ch_target // channel: [ [panel], sites, tsv] | ||
| ch_fasta // channel: [ [ref], fasta, fai] | ||
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| main: | ||
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| ch_versions = Channel.empty() | ||
| ch_multiqc_files = Channel.empty() | ||
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| ch_mpileup = ch_input | ||
| .combine(ch_target) | ||
| .map{metaI, bam, bai, metaP, sites, tsv -> | ||
| [metaI + metaP, bam, sites, tsv]} | ||
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| BCFTOOLS_MPILEUP( | ||
| ch_mpileup, | ||
| ch_fasta, | ||
| false | ||
| ) | ||
| ch_versions = ch_versions.mix(BCFTOOLS_MPILEUP.out.versions.first()) | ||
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| ch_output = BCFTOOLS_MPILEUP.out.vcf | ||
| .combine(BCFTOOLS_MPILEUP.out.tbi, by:0) | ||
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| ch_multiqc_files = ch_multiqc_files.mix(BCFTOOLS_MPILEUP.out.stats.map{ it[1] }) | ||
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| emit: | ||
| vcf = ch_output // channel: [ [id, panel], vcf, tbi ] | ||
| versions = ch_versions // channel: [ versions.yml ] | ||
| multiqc_files = ch_multiqc_files | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,90 +1,90 @@ | ||
| include { BCFTOOLS_VIEW as VIEW_VCF_SNPS } from '../../../modules/nf-core/bcftools/view/main.nf' | ||
| include { BCFTOOLS_VIEW as VIEW_VCF_SITES } from '../../../modules/nf-core/bcftools/view/main.nf' | ||
| include { BCFTOOLS_INDEX as VCF_INDEX1 } from '../../../modules/nf-core/bcftools/index/main.nf' | ||
| include { BCFTOOLS_INDEX as VCF_INDEX3 } from '../../../modules/nf-core/bcftools/index/main.nf' | ||
| include { BCFTOOLS_INDEX as VCF_INDEX4 } from '../../../modules/nf-core/bcftools/index/main.nf' | ||
| include { BCFTOOLS_INDEX as VCF_INDEX5 } from '../../../modules/nf-core/bcftools/index/main.nf' | ||
| include { BCFTOOLS_NORM } from '../../../modules/nf-core/bcftools/norm/main.nf' | ||
| include { BCFTOOLS_QUERY } from '../../../modules/nf-core/bcftools/query/main.nf' | ||
| include { TABIX_BGZIP } from '../../../modules/nf-core/tabix/bgzip/main' | ||
| include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix/main' | ||
| include { VCF_PHASE_SHAPEIT5 } from '../../../subworkflows/nf-core/vcf_phase_shapeit5/main' | ||
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| workflow GET_PANEL { | ||
| take: | ||
| ch_vcf // channel: [ [id], vcf, index ] | ||
| ch_fasta // channel: [ [genome], fasta, fai ] | ||
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| main: | ||
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| ch_versions = Channel.empty() | ||
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| BCFTOOLS_NORM(ch_vcf, ch_fasta.map{ genome, fasta, fai -> [genome, fasta] }) | ||
| ch_versions = ch_versions.mix(BCFTOOLS_NORM.out.versions.first()) | ||
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| // Extract only the SNP | ||
| VIEW_VCF_SNPS(BCFTOOLS_NORM.out.vcf // [ meta, vcf ] | ||
| .combine(Channel.of([[]])), [], [], []) | ||
| ch_versions = ch_versions.mix(VIEW_VCF_SNPS.out.versions.first()) | ||
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| VCF_INDEX3(VIEW_VCF_SNPS.out.vcf) | ||
| ch_versions = ch_versions.mix(VCF_INDEX3.out.versions.first()) | ||
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| ch_panel_norm = VIEW_VCF_SNPS.out.vcf | ||
| .combine(VCF_INDEX3.out.csi, by:0) | ||
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| // Extract sites positions | ||
| vcf_region = VIEW_VCF_SNPS.out.vcf | ||
| .combine(VCF_INDEX3.out.csi, by:0) | ||
| VIEW_VCF_SITES( ch_panel_norm, | ||
| [], [], []) | ||
| ch_versions = ch_versions.mix(VIEW_VCF_SITES.out.versions.first()) | ||
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| VCF_INDEX4(VIEW_VCF_SITES.out.vcf) | ||
| ch_versions = ch_versions.mix(VCF_INDEX4.out.versions.first()) | ||
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| ch_panel_sites = VIEW_VCF_SITES.out.vcf | ||
| .combine(VCF_INDEX4.out.csi, by:0) | ||
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| // Convert to TSV | ||
| BCFTOOLS_QUERY(ch_panel_sites, | ||
| [], [], []) | ||
| ch_versions = ch_versions.mix(BCFTOOLS_QUERY.out.versions.first()) | ||
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| TABIX_BGZIP(BCFTOOLS_QUERY.out.output) | ||
| ch_versions = ch_versions.mix(TABIX_BGZIP.out.versions.first()) | ||
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| TABIX_TABIX(TABIX_BGZIP.out.output) | ||
| ch_versions = ch_versions.mix(TABIX_TABIX.out.versions.first()) | ||
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| ch_panel_tsv = TABIX_BGZIP.out.output | ||
| .combine(TABIX_TABIX.out.tbi, by: 0) | ||
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| // Phase panel | ||
| if (params.phased == false) { | ||
| VCF_PHASE_SHAPEIT5(vcf_region | ||
| .map { meta, vcf, csi -> [meta, vcf, csi, [], meta.region] }, | ||
| Channel.of([[],[],[]]).collect(), | ||
| Channel.of([[],[],[]]).collect(), | ||
| Channel.of([[],[]]).collect()) | ||
| ch_versions = ch_versions.mix(VCF_PHASE_SHAPEIT5.out.versions.first()) | ||
| ch_panel_phased = VCF_PHASE_SHAPEIT5.out.variants_phased | ||
| .combine(VCF_PHASE_SHAPEIT5.out.variants_index, by: 0) | ||
| } else { | ||
| ch_panel_phased = VIEW_VCF_SNPS.out.vcf | ||
| .combine(VCF_INDEX3.out.csi, by: 0) | ||
| } | ||
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| ch_panel = ch_panel_norm | ||
| .combine(ch_panel_sites, by: 0) | ||
| .combine(ch_panel_tsv, by: 0) | ||
| .combine(ch_panel_phased, by: 0) | ||
| .map{ metaI, norm, n_index, sites, s_index, tsv, t_index, phased, p_index | ||
| -> [[panel:metaI.id], norm, n_index, sites, s_index, tsv, t_index, phased, p_index] | ||
| } | ||
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| emit: | ||
| panel = ch_panel // channel: [ [panel], norm, n_index, sites, s_index, tsv, t_index, phased, p_index] | ||
| versions = ch_versions // channel: [ versions.yml ] | ||
| } | ||
| include { BCFTOOLS_VIEW as VIEW_VCF_SNPS } from '../../../modules/nf-core/bcftools/view/main.nf' | ||
| include { BCFTOOLS_VIEW as VIEW_VCF_SITES } from '../../../modules/nf-core/bcftools/view/main.nf' | ||
| include { BCFTOOLS_INDEX as VCF_INDEX1 } from '../../../modules/nf-core/bcftools/index/main.nf' | ||
| include { BCFTOOLS_INDEX as VCF_INDEX3 } from '../../../modules/nf-core/bcftools/index/main.nf' | ||
| include { BCFTOOLS_INDEX as VCF_INDEX4 } from '../../../modules/nf-core/bcftools/index/main.nf' | ||
| include { BCFTOOLS_INDEX as VCF_INDEX5 } from '../../../modules/nf-core/bcftools/index/main.nf' | ||
| include { BCFTOOLS_NORM } from '../../../modules/nf-core/bcftools/norm/main.nf' | ||
| include { BCFTOOLS_QUERY } from '../../../modules/nf-core/bcftools/query/main.nf' | ||
| include { TABIX_BGZIP } from '../../../modules/nf-core/tabix/bgzip/main' | ||
| include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix/main' | ||
| include { VCF_PHASE_SHAPEIT5 } from '../../../subworkflows/nf-core/vcf_phase_shapeit5/main' | ||
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| workflow GET_PANEL { | ||
| take: | ||
| ch_vcf // channel: [ [id], vcf, index ] | ||
| ch_fasta // channel: [ [genome], fasta, fai ] | ||
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| main: | ||
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| ch_versions = Channel.empty() | ||
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| BCFTOOLS_NORM(ch_vcf, ch_fasta.map{ genome, fasta, fai -> [genome, fasta] }) | ||
| ch_versions = ch_versions.mix(BCFTOOLS_NORM.out.versions.first()) | ||
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| // Extract only the SNP | ||
| VIEW_VCF_SNPS(BCFTOOLS_NORM.out.vcf // [ meta, vcf ] | ||
| .combine(Channel.of([[]])), [], [], []) | ||
| ch_versions = ch_versions.mix(VIEW_VCF_SNPS.out.versions.first()) | ||
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| VCF_INDEX3(VIEW_VCF_SNPS.out.vcf) | ||
| ch_versions = ch_versions.mix(VCF_INDEX3.out.versions.first()) | ||
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| ch_panel_norm = VIEW_VCF_SNPS.out.vcf | ||
| .combine(VCF_INDEX3.out.csi, by:0) | ||
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| // Extract sites positions | ||
| vcf_region = VIEW_VCF_SNPS.out.vcf | ||
| .combine(VCF_INDEX3.out.csi, by:0) | ||
| VIEW_VCF_SITES( ch_panel_norm, | ||
| [], [], []) | ||
| ch_versions = ch_versions.mix(VIEW_VCF_SITES.out.versions.first()) | ||
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| VCF_INDEX4(VIEW_VCF_SITES.out.vcf) | ||
| ch_versions = ch_versions.mix(VCF_INDEX4.out.versions.first()) | ||
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| ch_panel_sites = VIEW_VCF_SITES.out.vcf | ||
| .combine(VCF_INDEX4.out.csi, by:0) | ||
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| // Convert to TSV | ||
| BCFTOOLS_QUERY(ch_panel_sites, | ||
| [], [], []) | ||
| ch_versions = ch_versions.mix(BCFTOOLS_QUERY.out.versions.first()) | ||
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| TABIX_BGZIP(BCFTOOLS_QUERY.out.output) | ||
| ch_versions = ch_versions.mix(TABIX_BGZIP.out.versions.first()) | ||
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| TABIX_TABIX(TABIX_BGZIP.out.output) | ||
| ch_versions = ch_versions.mix(TABIX_TABIX.out.versions.first()) | ||
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| ch_panel_tsv = TABIX_BGZIP.out.output | ||
| .combine(TABIX_TABIX.out.tbi, by: 0) | ||
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| // Phase panel | ||
| if (params.phased == false) { | ||
| VCF_PHASE_SHAPEIT5(vcf_region | ||
| .map { meta, vcf, csi -> [meta, vcf, csi, [], meta.region] }, | ||
| Channel.of([[],[],[]]).collect(), | ||
| Channel.of([[],[],[]]).collect(), | ||
| Channel.of([[],[]]).collect()) | ||
| ch_versions = ch_versions.mix(VCF_PHASE_SHAPEIT5.out.versions.first()) | ||
| ch_panel_phased = VCF_PHASE_SHAPEIT5.out.variants_phased | ||
| .combine(VCF_PHASE_SHAPEIT5.out.variants_index, by: 0) | ||
| } else { | ||
| ch_panel_phased = VIEW_VCF_SNPS.out.vcf | ||
| .combine(VCF_INDEX3.out.csi, by: 0) | ||
| } | ||
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| ch_panel = ch_panel_norm | ||
| .combine(ch_panel_sites, by: 0) | ||
| .combine(ch_panel_tsv, by: 0) | ||
| .combine(ch_panel_phased, by: 0) | ||
| .map{ metaI, norm, n_index, sites, s_index, tsv, t_index, phased, p_index | ||
| -> [[panel:metaI.id], norm, n_index, sites, s_index, tsv, t_index, phased, p_index] | ||
| } | ||
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| emit: | ||
| panel = ch_panel // channel: [ [panel], norm, n_index, sites, s_index, tsv, t_index, phased, p_index] | ||
| versions = ch_versions // channel: [ versions.yml ] | ||
| } |
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