From fd311028a85b24484a014c83dc565ea296390345 Mon Sep 17 00:00:00 2001
From: Nicholas Minor <nrminor@wisc.edu>
Date: Thu, 7 Nov 2024 14:42:40 -0600
Subject: [PATCH] publishing run command alongside each workflow's results so
 multiple run commands can be published

---
 conf/illumina.config | 3 +++
 conf/nanopore.config | 3 +++
 modules/reporting.nf | 2 +-
 3 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/conf/illumina.config b/conf/illumina.config
index 5b9f677..e84f6fc 100644
--- a/conf/illumina.config
+++ b/conf/illumina.config
@@ -12,6 +12,9 @@ params {
     // split off ont results
     params.illumina_results = params.results + "/illumina"
 
+    // Where to place the Nanopore workflow run command
+    run_command = params.illumina_results
+
     // paired read merging
     merged = params.illumina_results + "/01_merged_reads"
 
diff --git a/conf/nanopore.config b/conf/nanopore.config
index 6e66f5f..7d3252e 100644
--- a/conf/nanopore.config
+++ b/conf/nanopore.config
@@ -12,6 +12,9 @@ params {
     // split off ont results
     params.ont_results = params.results + "/nanopore"
 
+    // Where to place the Nanopore workflow run command
+    run_command = params.ont_results
+
     // basecalling and demultiplexing results
     basecall_results = params.ont_results + "/01_basecalled_demuxed"
     basecall_bams = params.basecall_results + "/bams"
diff --git a/modules/reporting.nf b/modules/reporting.nf
index e100cf1..6de38bf 100644
--- a/modules/reporting.nf
+++ b/modules/reporting.nf
@@ -30,7 +30,7 @@ process PUBLISH_COMMAND {
 
     /* */
 
-    publishDir params.results, mode: "copy", overwrite: true
+    publishDir params.run_command, mode: "copy", overwrite: true
 
 	errorStrategy { task.attempt < 2 ? 'retry' : 'ignore' }
 	maxRetries 1