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)

main.nf

@@ -84,8 +84,11 @@ include { muse } from './module/muse' addParams(
 
 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}"
-    )
+    workflow_log_output_dir: "${params.log_output_dir}/process-log/intersect-BCFtools-${params.BCFtools_version}",
+    output_filename: generate_standard_filename("Intersect",
+        params.dataset_id,
+        params.sample_id,
+        [:]))
 
 // Returns the index file for the given bam or vcf
 def indexFile(bam_or_vcf) {

module/intersect-processes.nf

@@ -74,3 +74,33 @@ process intersect_VCFs_BCFtools {
      Rscript ${script_dir}/plot-venn.R --isec_dir ${isec_dir} --dataset ${params.dataset_id}
      """
      }
+
+process concat_VCFs_BCFtools {
+    container params.docker_image_BCFtools
+    publishDir path: "${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: { "${task.process.replace(':', '/')}-${task.index}/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 +1,12 @@
 include { generate_sha512sum } from './common'
-include { intersect_VCFs_BCFtools; plot_venn_R } from './intersect-processes.nf'
+include { intersect_VCFs_BCFtools; plot_venn_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
+        ])
 
 workflow intersect {
     // pass bin directory in project folder as channel into docker
@@ -16,16 +23,29 @@ workflow intersect {
             params.intersect_regions,
             params.intersect_regions_index
             )
+        plot_venn_R(
+            script_dir_ch,
+            intersect_VCFs_BCFtools.out.isec_dir
+            )
+        concat_VCFs_BCFtools(
+            intersect_VCFs_BCFtools.out.consensus_vcf,
+            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_venn_R(
-            script_dir_ch,
-            intersect_VCFs_BCFtools.out.isec_dir,
-        )
     }