Merge pull request #116 from naobservatory/harmon_fix_copying_file_bug

Fixing bug that's causing a fatal error in master pipeline.
naobservatory · Nov 27, 2024 · 829e2d4 · 829e2d4
2 parents b75ddc6 + 59851ff
commit 829e2d4
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git 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
@@ -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"