From 59851ff73f0d2204fea7aaab4ccc1b08bd29398c Mon Sep 17 00:00:00 2001
From: EC2 Default User <harmonprograms@protonmail.com>
Date: Wed, 27 Nov 2024 19:53:47 +0000
Subject: [PATCH] From the way nextflow is setup, it doesn't work if we use
 '{workDir}', however if we use what the working directory is set to
 '{params.base_dir}/work', it seems to have no issue.

---
 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 b8f36e9..899bef2 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"