Sfitz concat vcf

CHANGELOG.md

@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [Unreleased]
 
 ### Added
+- Add concatenation of consensus variants to one VCF
 - Add variant intersection Venn diagram
 - Add regions filter to variant intersections
 - Add second BCFtools step to create full presence/absence variant table (including private)
@@ -15,8 +16,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add `split_VCF_bcftools` to `Mutect2` workflow, separating SNVs, MNVs and Indels
 
 ### Changed
-- reconfigure `intersect_regions` to use all contigs except `decoy`
-- reconfigure `call_regions` to `intersect_regions` 
+- Update resource allocation to include new processes
+- Reconfigure `intersect_regions` to use all contigs except `decoy`
+- Reconfigure `call_regions` to `intersect_regions` 
 - Update to BCFtools v1.17
 - Keep `bam-readcount` output in `SomaticSniper` QC folder
 - Update `MuSE` to `v2.0.2`

config/F16.config

@@ -1,4 +1,4 @@
-// Other processes after create_IndelCandidate_SAMtools will only run one at a time, so
+// Other processes will only run one at a time, so
 // we don't need to control their resources.
 
 process {
@@ -78,4 +78,24 @@ process {
             }
         }
     }
+    withName: plot_VennDiagram_R {
+        cpus = 2
+        memory = 5.GB
+        retry_strategy {
+            memory {
+                strategy = 'add'
+                operand = 10.GB
+            }
+        }
+    }
+    withName: concat_VCFs_BCFtools {
+        cpus = 2
+        memory = 5.GB
+        retry_strategy {
+            memory {
+                strategy = 'add'
+                operand = 10.GB
+            }
+        }
+    }
 }

config/F2.config

@@ -26,4 +26,12 @@ process {
     withName: call_sSNV_Strelka2 {
         cpus = 2
     }
+    withName: plot_VennDiagram_R {
+        cpus = 2
+        memory = 1.GB
+    }
+    withName: concat_VCFs_BCFtools {
+        cpus = 2
+        memory = 2.GB
+    }
 }

config/F32.config

@@ -78,4 +78,24 @@ process {
             }
         }
     }
+    withName: plot_VennDiagram_R {
+        cpus = 2
+        memory = 5.GB
+        retry_strategy {
+            memory {
+                strategy = 'add'
+                operand = 10.GB
+            }
+        }
+    }
+    withName: concat_VCFs_BCFtools {
+        cpus = 2
+        memory = 5.GB
+        retry_strategy {
+            memory {
+                strategy = 'add'
+                operand = 10.GB
+            }
+        }
+    }
 }

config/F72.config

@@ -78,4 +78,24 @@ process {
             }
         }
     }
+    withName: plot_VennDiagram_R {
+        cpus = 2
+        memory = 5.GB
+        retry_strategy {
+            memory {
+                strategy = 'add'
+                operand = 10.GB
+            }
+        }
+    }
+    withName: concat_VCFs_BCFtools {
+        cpus = 2
+        memory = 5.GB
+        retry_strategy {
+            memory {
+                strategy = 'add'
+                operand = 10.GB
+            }
+        }
+    }
 }

config/M64.config

@@ -78,4 +78,24 @@ process {
             }
         }
     }
+        withName: plot_VennDiagram_R {
+        cpus = 2
+        memory = 5.GB
+        retry_strategy {
+            memory {
+                strategy = 'add'
+                operand = 10.GB
+            }
+        }
+    }
+    withName: concat_VCFs_BCFtools {
+        cpus = 2
+        memory = 5.GB
+        retry_strategy {
+            memory {
+                strategy = 'add'
+                operand = 10.GB
+            }
+        }
+    }
 }

main.nf

@@ -63,29 +63,29 @@ include { somaticsniper } from './module/somaticsniper' addParams(
 include { strelka2 } from './module/strelka2' addParams(
     workflow_output_dir: "${params.output_dir_base}/Strelka2-${params.strelka2_version}",
     workflow_log_output_dir: "${params.log_output_dir}/process-log/Strelka2-${params.strelka2_version}",
-    output_filename: generate_standard_filename("Strelka2_${params.strelka2_version}",
+    output_filename: generate_standard_filename("Strelka2-${params.strelka2_version}",
         params.dataset_id,
         params.sample_id,
         [:]))
 include { mutect2 } from './module/mutect2' addParams(
     workflow_output_dir: "${params.output_dir_base}/Mutect2-${params.GATK_version}",
     workflow_log_output_dir: "${params.log_output_dir}/process-log/Mutect2-${params.GATK_version}",
-    output_filename: generate_standard_filename("Mutect2_${params.GATK_version}",
+    output_filename: generate_standard_filename("Mutect2-${params.GATK_version}",
         params.dataset_id,
         params.sample_id,
         [:]))
 include { muse } from './module/muse' addParams(
     workflow_output_dir: "${params.output_dir_base}/MuSE-${params.MuSE_version}",
     workflow_log_output_dir: "${params.log_output_dir}/process-log/MuSE-${params.MuSE_version}",
-    output_filename: generate_standard_filename("MuSE_${params.MuSE_version}",
+    output_filename: generate_standard_filename("MuSE-${params.MuSE_version}",
         params.dataset_id,
         params.sample_id,
         [:]))
 
 include { intersect } from './module/intersect' addParams(
     workflow_output_dir: "${params.output_dir_base}/intersect-BCFtools-${params.BCFtools_version}",
     workflow_log_output_dir: "${params.log_output_dir}/process-log/intersect-BCFtools-${params.BCFtools_version}",
-    output_filename: generate_standard_filename("Consensus",
+    output_filename: generate_standard_filename("BCFtools-${params.BCFtools_version}",
         params.dataset_id,
         params.sample_id,
         [:]))

module/intersect-processes.nf

@@ -14,14 +14,16 @@ process intersect_VCFs_BCFtools {
         pattern: "*.vcf.gz*"
     publishDir path: "${params.workflow_output_dir}/output",
         mode: "copy",
-        pattern: "isec-2-or-more"
+        pattern: "isec-2-or-more/*.txt",
+        saveAs: { "${file(it).getParent().getName()}/${params.output_filename}_${file(it).getName()}" }
     publishDir path: "${params.workflow_output_dir}/output",
         mode: "copy",
-        pattern: "isec-1-or-more/*.txt"
+        pattern: "isec-1-or-more/*.txt",
+        saveAs: { "${file(it).getParent().getName()}/${params.output_filename}_${file(it).getName()}" }
     publishDir path: "${params.workflow_log_output_dir}",
         mode: "copy",
         pattern: ".command.*",
-        saveAs: { "${task.process.replace(':', '/')}-${task.index}/log${file(it).getName()}" }
+        saveAs: { "${task.process.replace(':', '/')}/log${file(it).getName()}" }
 
     input:
     path vcfs
@@ -33,8 +35,8 @@ process intersect_VCFs_BCFtools {
     path "*.vcf.gz", emit: consensus_vcf
     path "*.vcf.gz.tbi", emit: consensus_idx
     path ".command.*"
-    path "isec-2-or-more"
-    path "isec-1-or-more", emit: isec_dir
+    path "isec-2-or-more/*.txt"
+    path "isec-1-or-more/*.txt", emit: isec
 
     script:
     vcf_list = vcfs.join(' ')
@@ -58,11 +60,11 @@ process intersect_VCFs_BCFtools {
      publishDir path: "${params.workflow_log_output_dir}",
          mode: "copy",
          pattern: ".command.*",
-         saveAs: { "${task.process.replace(':', '/')}-${task.index}/log${file(it).getName()}" }
+         saveAs: { "${task.process.replace(':', '/')}/log${file(it).getName()}" }
 
      input:
      path script_dir
-     path isec_dir
+     path isec
 
      output:
      path ".command.*"
@@ -71,6 +73,36 @@ process intersect_VCFs_BCFtools {
      script:
      """
      set -euo pipefail
-     Rscript ${script_dir}/plot-venn.R --isec_dir ${isec_dir} --outfile ${params.output_filename}_Venn-diagram.tiff
+     Rscript ${script_dir}/plot-venn.R --isec_readme README.txt --isec_sites sites.txt --outfile ${params.output_filename}_Venn-diagram.tiff
      """
      }
+
+process concat_VCFs_BCFtools {
+    container params.docker_image_BCFtools
+    publishDir path: "${params.workflow_output_dir}/intermediate/${task.process.split(':')[-1]}",
+        mode: "copy",
+        pattern: "*concat.vcf",
+        enabled: params.save_intermediate_files
+    publishDir path: "${params.workflow_log_output_dir}",
+        mode: "copy",
+        pattern: ".command.*",
+        saveAs: { "${task.process.replace(':', '/')}/log${file(it).getName()}" }
+
+    input:
+    path vcfs
+    path indices
+
+    output:
+    path "*concat.vcf", emit: concat_vcf
+    path ".command.*"
+
+    script:
+    vcf_list = vcfs.join(' ')
+    """
+    set -euo pipefail
+    # BCFtools concat to create a single VCF with all nfiles +2 variants
+    # output header is a uniquified concatenation of all headers
+    # output `INFO` `FORMAT` `NORMAL` and `TUMOR` fields are from the first listed VCF that has the variant
+    bcftools concat --output-type v --output ${params.output_filename}_SNV-concat.vcf --allow-overlaps --rm-dups all ${vcf_list}
+    """
+    }

module/intersect.nf

@@ -1,5 +1,19 @@
 include { generate_sha512sum } from './common'
-include { intersect_VCFs_BCFtools; plot_VennDiagram_R } from './intersect-processes.nf'
+include { intersect_VCFs_BCFtools; plot_VennDiagram_R; concat_VCFs_BCFtools } from './intersect-processes.nf'
+include { compress_index_VCF } from '../external/pipeline-Nextflow-module/modules/common/index_VCF_tabix/main.nf' addParams(
+    options: [
+        output_dir: params.workflow_output_dir,
+        log_output_dir: params.workflow_log_output_dir,
+        bgzip_extra_args: params.bgzip_extra_args,
+        tabix_extra_args: params.tabix_extra_args
+        ])
+def sortVcfs(List paths) {
+    paths.sort { a, b ->
+        def toolA = file(a).getName()
+        def toolB = file(b).getName()
+        return toolA.compareTo(toolB)
+    }
+}
 
 workflow intersect {
     take:
@@ -8,22 +22,39 @@ workflow intersect {
     script_dir_ch
 
     main:
+        vcfs_ch = tool_vcfs
+            .map { sortVcfs(it)  }
         intersect_VCFs_BCFtools(
-            tool_vcfs,
+            vcfs_ch,
             tool_indices,
             params.intersect_regions,
             params.intersect_regions_index
             )
+        plot_VennDiagram_R(
+            script_dir_ch,
+            intersect_VCFs_BCFtools.out.isec,
+            )
+        consensus_vcfs_ch = intersect_VCFs_BCFtools.out.consensus_vcf
+            .map { sortVcfs(it) }
+        concat_VCFs_BCFtools(
+            consensus_vcfs_ch,
+            intersect_VCFs_BCFtools.out.consensus_idx
+            )
+        compress_index_VCF(concat_VCFs_BCFtools.out.concat_vcf
+            .map{ it -> ['SNV', it]}
+            )
         file_for_sha512 = intersect_VCFs_BCFtools.out.consensus_vcf
             .flatten()
             .map{ it -> ["${file(it).getName().split('_')[0]}-SNV-vcf", it]}
             .mix(intersect_VCFs_BCFtools.out.consensus_idx
                 .flatten()
                 .map{ it -> ["${file(it).getName().split('_')[0]}-SNV-idx", it]}
                 )
+            .mix(compress_index_VCF.out.index_out
+                .map{ it -> ["intersect-${it[0]}-vcf", it[1]] }
+                )
+            .mix(compress_index_VCF.out.index_out
+                .map{ it -> ["intersect-${it[0]}-index", it[2]] }
+                )
         generate_sha512sum(file_for_sha512)
-        plot_VennDiagram_R(
-            script_dir_ch,
-            intersect_VCFs_BCFtools.out.isec_dir,
-        )
     }

r-scripts/plot-venn.R

@@ -1,8 +1,9 @@
 # Script to plot a Venn diagram of shared variants from the different SNV calling algorithms, using the output of BCFtools isec
 # Initial commit: Sorel Fitz-Gibbon 2023-06-29
 # Input:
-#  -i, --isec_dir: The directory containing the output from BCFtools intersect
-#  -d, --dataset: The dataset ID passed from nextflow
+#  -r, --isec_readme: The README.txt file from BCFtools intersect
+#  -s, --isec_sites: The sites.txt file from BCFtools intersect
+#  -o, --outfile: The output filename
 # Output:
 # - A Venn diagram of shared variant counts from the BCFtools intersection of the VCF files
 
@@ -12,7 +13,8 @@ library('VennDiagram');
 
 ## Parse the arguments #############################################################################
 parser <- ArgumentParser();
-parser$add_argument('-i', '--isec_dir', help = 'The directory containing the output from BCFtools intersect', type = 'character');
+parser$add_argument('-r', '--isec_readme', help = 'The README.txt file from BCFtools intersect', type = 'character');
+parser$add_argument('-s', '--isec_sites', help = 'The sites.txt file from BCFtools intersect', type = 'character');
 parser$add_argument('-o', '--outfile', help = 'Output filename', type = 'character');
 args <- parser$parse_args();
 
@@ -31,20 +33,24 @@ plot.venn <- function(tool.variants, outfile) {
 
 ### Main ###########################################################################################
 # Get intersection counts from BCFtools isec output and format for plotting
-algorithms <- readLines(paste0(args$isec_dir,'/README.txt'));
-algorithms <- algorithms[grep(paste0('^', args$isec_dir), algorithms)];
-algorithms <- gsub(paste0(args$isec_dir,'.*\t'), '', algorithms);
+algorithms <- readLines(args$isec_readme);
+algorithms <- algorithms[grep('^isec-1-or-more', algorithms)];
+algorithms <- gsub('isec-1-or-more.*\t', '', algorithms);
 algorithms <- gsub('-.*', '', algorithms);
-sites <- read.table(paste0(args$isec_dir,'/sites.txt'), header = FALSE, colClasses = 'character');
+
+sites <- read.table(args$isec_sites, header = FALSE, colClasses = 'character');
 split.col <- strsplit(as.character(sites$V5), '');
 sites$col1 <- sapply(split.col, '[', 1);
 sites$col2 <- sapply(split.col, '[', 2);
 sites$col3 <- sapply(split.col, '[', 3);
 sites$col4 <- sapply(split.col, '[', 4);
 sites$V5 <- NULL;
+
 header <- c('chrom', 'pos', 'ref', 'alt', algorithms);
 colnames(sites) <- header
+
 variants <- paste(sites$chrom, sites$pos, sep = '_');
-tool.variants <- lapply(sites[, algorithms], function(x) variants[x == 1])
+tool.variants <- lapply(sites[, algorithms], function(x) variants[x == 1]);
 tool.variants.ordered <- tool.variants[order(lengths(tool.variants), decreasing = TRUE)];
+
 plot.venn(tool.variants.ordered, args$outfile);