Sfitz concat vcf

main.nf

@@ -85,7 +85,7 @@ 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}",
-    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

@@ -15,6 +15,9 @@ process intersect_VCFs_BCFtools {
     publishDir path: "${params.workflow_output_dir}/output",
         mode: "copy",
         pattern: "isec-2-or-more"
+    publishDir path: "${params.workflow_output_dir}/output",
+        mode: "copy",
+        pattern: "isec-1-or-more/*.txt"
     publishDir path: "${params.workflow_log_output_dir}",
         mode: "copy",
         pattern: ".command.*",
@@ -31,7 +34,7 @@ process intersect_VCFs_BCFtools {
     path "*.vcf.gz.tbi", emit: consensus_idx
     path ".command.*"
     path "isec-2-or-more"
-    path "isec-1-or-more", emit: isec_dir
+    path "isec-1-or-more/*.txt", emit: isec
 
     script:
     vcf_list = vcfs.join(' ')
@@ -52,27 +55,23 @@ process intersect_VCFs_BCFtools {
      publishDir path: "${params.workflow_output_dir}/output",
          mode: "copy",
          pattern: "*.tiff"
-    publishDir path: "${params.workflow_output_dir}/output",
-        mode: "copy",
-        pattern: "isec-1-or-more/*.txt"
      publishDir path: "${params.workflow_log_output_dir}",
          mode: "copy",
          pattern: ".command.*",
          saveAs: { "${task.process.replace(':', '/')}/log${file(it).getName()}" }
 
      input:
      path script_dir
-     path isec_dir
+     path isec
 
      output:
-     path "isec-1-or-more/*.txt"
      path ".command.*"
      path "*.tiff"
 
      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
      """
      }
 

module/intersect.nf

@@ -23,7 +23,7 @@ workflow intersect {
             )
         plot_VennDiagram_R(
             script_dir_ch,
-            intersect_VCFs_BCFtools.out.isec_dir,
+            intersect_VCFs_BCFtools.out.isec,
             )
         concat_VCFs_BCFtools(
             intersect_VCFs_BCFtools.out.consensus_vcf,

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 directory containing the output from BCFtools intersect', type = 'character');
+parser$add_argument('-s', '--isec_sites', help = 'The directory containing the output from BCFtools intersect', type = 'character');
 parser$add_argument('-o', '--outfile', help = 'Output filename', type = 'character');
 args <- parser$parse_args();
 
@@ -31,11 +33,11 @@ plot.venn <- function(tool.variants, outfile) {
 
 ### Main ###########################################################################################
 # Get intersection counts from BCFtools isec output and format for plotting
-algorithms <- readLines(file.path(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(file.path(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);