From 30a2a6e910e30a15dd6fa41f59cf14dc85d633c5 Mon Sep 17 00:00:00 2001
From: Will Bradshaw <wjbradshaw1@gmail.com>
Date: Wed, 27 Nov 2024 16:21:48 -0500
Subject: [PATCH] Merge pull request #116 from
 naobservatory/harmon_fix_copying_file_bug

Fixing bug that's causing a fatal error in master pipeline.
---
 workflows/run.nf            | 4 ++--
 workflows/run_validation.nf | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/workflows/run.nf b/workflows/run.nf
index c0acece..6793ea9 100644
--- a/workflows/run.nf
+++ b/workflows/run.nf
@@ -84,9 +84,9 @@ workflow RUN {
     time_ch = Channel.of(start_time_str + "\n").collectFile(name: "time.txt")
     version_ch = Channel.fromPath("${projectDir}/pipeline-version.txt")
     index_params_ch = Channel.fromPath("${params.ref_dir}/input/index-params.json")
-    .map { file -> file.copyTo("${workDir}/params-index.json") }
+    .map { file -> file.copyTo("${params.base_dir}/work/params-index.json") }
     index_pipeline_version_ch = Channel.fromPath("${params.ref_dir}/logging/pipeline-version.txt")
-    .map { file -> file.copyTo("${workDir}/pipeline-version-index.txt") }
+    .map { file -> file.copyTo("${params.base_dir}/work/pipeline-version-index.txt") }
     publish:
         // Saved inputs
         index_params_ch >> "input"
diff --git a/workflows/run_validation.nf b/workflows/run_validation.nf
index 66e55ca..c0cdf32 100644
--- a/workflows/run_validation.nf
+++ b/workflows/run_validation.nf
@@ -43,9 +43,9 @@ workflow RUN_VALIDATION {
     time_ch = Channel.of(start_time_str + "\n").collectFile(name: "time.txt")
     version_ch = Channel.fromPath("${projectDir}/pipeline-version.txt")
     index_params_ch = Channel.fromPath("${params.ref_dir}/input/index-params.json")
-    .map { file -> file.copyTo("${workDir}/params-index.json") }
+    .map { file -> file.copyTo("${params.base_dir}/work/params-index.json") }
     index_pipeline_version_ch = Channel.fromPath("${params.ref_dir}/logging/pipeline-version.txt")
-    .map { file -> file.copyTo("${workDir}/pipeline-version-index.txt") }
+    .map { file -> file.copyTo("${params.base_dir}/work/pipeline-version-index.txt") }
     publish:
         // Saved inputs
         index_params_ch >> "input"