From 46363987aae3a330eed26f127a11b52f4d302f3b Mon Sep 17 00:00:00 2001
From: Sam Nicholls <sam.nicholls@nanoporetech.com>
Date: Mon, 9 Sep 2024 18:41:17 +0000
Subject: [PATCH] Output dtu_plots to local work dir then mv [CW-4886]

---
 bin/plot_dtu_results.R                  | 2 +-
 subworkflows/differential_expression.nf | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/bin/plot_dtu_results.R b/bin/plot_dtu_results.R
index 212e1aa..12850b1 100755
--- a/bin/plot_dtu_results.R
+++ b/bin/plot_dtu_results.R
@@ -44,7 +44,7 @@ sig_level <- 0.05
 genes <- as.character(tdf[which(tdf$p_gene < sig_level),]$gene_id)
 genes <- unique(genes)
 
-pdf("de_analysis/dtu_plots.pdf")
+pdf("dtu_plots.pdf")
 
 for(gene in genes){
     gdf<-tdf[which(tdf$gene_id==gene),]
diff --git a/subworkflows/differential_expression.nf b/subworkflows/differential_expression.nf
index 7f85667..ff42950 100644
--- a/subworkflows/differential_expression.nf
+++ b/subworkflows/differential_expression.nf
@@ -106,6 +106,8 @@ process plotResults {
         path "de_analysis/results_dtu.pdf", emit: dtu_pdf
     """
     plot_dtu_results.R
+    # output plots to common analysis output directory
+    mv dtu_plots.pdf de_analysis/dtu_plots.pdf
     """
 }