From 027f02c716ebc7e15475e9153049a7c4d475e51e Mon Sep 17 00:00:00 2001
From: Sorel Fitz-Gibbon <sfitzgibbon@mednet.ucla.edu>
Date: Tue, 8 Aug 2023 10:41:39 -0700
Subject: [PATCH] fix standardized isec output and spacing in rscript

---
 module/intersect-processes.nf | 10 +++++-----
 r-scripts/plot-venn.R         |  4 ++++
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/module/intersect-processes.nf b/module/intersect-processes.nf
index 12e64fb5..105b6a09 100644
--- a/module/intersect-processes.nf
+++ b/module/intersect-processes.nf
@@ -12,14 +12,14 @@ process intersect_VCFs_BCFtools {
     publishDir path: "${params.workflow_output_dir}/output",
         mode: "copy",
         pattern: "*.vcf.gz*"
-    publishDir path: "${params.workflow_output_dir}/output",
+    publishDir path: "${params.workflow_output_dir}/output/isec-2-or-more",
         mode: "copy",
         pattern: "isec-2-or-more/*.txt",
-        saveAs: { "${params.output_filename}${file(it).getName()}" }
-    publishDir path: "${params.workflow_output_dir}/output",
+        saveAs: { "${params.output_filename}_${file(it).getName()}" }
+    publishDir path: "${params.workflow_output_dir}/output/isec-1-or-more",
         mode: "copy",
         pattern: "isec-1-or-more/*.txt",
-        saveAs: { "${params.output_filename}${file(it).getName()}" }
+        saveAs: { "${params.output_filename}_${file(it).getName()}" }
     publishDir path: "${params.workflow_log_output_dir}",
         mode: "copy",
         pattern: ".command.*",
@@ -35,7 +35,7 @@ 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-2-or-more/*.txt"
     path "isec-1-or-more/*.txt", emit: isec
 
     script:
diff --git a/r-scripts/plot-venn.R b/r-scripts/plot-venn.R
index 0cf6db69..8410907f 100644
--- a/r-scripts/plot-venn.R
+++ b/r-scripts/plot-venn.R
@@ -37,6 +37,7 @@ algorithms <- readLines(args$isec_readme);
 algorithms <- algorithms[grep('^isec-1-or-more', algorithms)];
 algorithms <- gsub('isec-1-or-more.*\t', '', algorithms);
 algorithms <- gsub('-.*', '', algorithms);
+
 sites <- read.table(args$isec_sites, header = FALSE, colClasses = 'character');
 split.col <- strsplit(as.character(sites$V5), '');
 sites$col1 <- sapply(split.col, '[', 1);
@@ -44,9 +45,12 @@ 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.ordered <- tool.variants[order(lengths(tool.variants), decreasing = TRUE)];
+
 plot.venn(tool.variants.ordered, args$outfile);