From ee64fc721ba182b8a43289731bd3cae514cbec49 Mon Sep 17 00:00:00 2001
From: Rachel Colquhoun <rachel.colquhoun@ed.ac.uk>
Date: Fri, 3 Nov 2023 13:04:38 +0000
Subject: [PATCH] output all files from output directory

---
 main.nf | 15 +++++----------
 1 file changed, 5 insertions(+), 10 deletions(-)

diff --git a/main.nf b/main.nf
index 4c5473f..27ffb0b 100644
--- a/main.nf
+++ b/main.nf
@@ -1,6 +1,6 @@
 process run_piranha {
 
-    publishDir "${params.out_dir}", mode: 'copy'
+    publishDir "${params.out_dir}", mode: 'copy', saveAs: {  fn -> fn.replace("piranha_output/", "")}
 
     container "${params.wf.container}:${workflow.manifest.version}"
 
@@ -9,10 +9,7 @@ process run_piranha {
         path run_dir
 
     output:
-        path "piranha_report.html"
-        path "barcode_reports"
-        path "detailed_run_report.csv"
-        path "published_data"
+        path "piranha_output/*"
 
     script:
     extra = ""
@@ -36,13 +33,11 @@ process run_piranha {
         extra += " --run-phylo"
     if ( params.supplementary_sequences )
         extra += " --supplementary-sequences ${params.supplementary_sequences}"
-     if ( params.supplementary_metadata )
-            extra += " --supplementary-metadata ${params.supplementary_metadata}"
+    if ( params.supplementary_metadata )
+        extra += " --supplementary-metadata ${params.supplementary_metadata}"
     """
     piranha -b ${barcodes_csv} -i ${run_dir} -o piranha_output --tempdir piranha_tmp -t ${task.cpus} ${extra}
-    mv piranha_output/* .
-    rm -rf piranha_output
-    mv report.html piranha_report.html
+    mv piranha_output/report.html piranha_output/piranha_report.html
     """
 
 }