Add 'ext capture_logs: false' to all processes

uclahs-cds · May 20, 2024 · 0b58ef9 · 0b58ef9
1 parent 4597ebc
commit 0b58ef9
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Showing 4 changed files with 13 additions and 1 deletion.
diff --git a/modules/PipeVal/generate-checksum/main.nf b/modules/PipeVal/generate-checksum/main.nf
@@ -30,6 +30,9 @@ process generate_checksum_PipeVal {
         pattern: "*.${options.checksum_alg}",
         mode: "copy" 
 
+    // This process uses the publishDir method to save the log files
+    ext capture_logs: false
+
     input:
         path(input_file)
 

diff --git a/modules/PipeVal/validate/main.nf b/modules/PipeVal/validate/main.nf
@@ -24,6 +24,9 @@ process run_validate_PipeVal {
         mode: "copy",
         saveAs: { "${task.process.split(':')[-1]}/${task.process.split(':')[-1]}-${task.index}/log${file(it).getName()}" }
 
+    // This process uses the publishDir method to save the log files
+    ext capture_logs: false
+
     input:
         path(file_to_validate)
 

diff --git a/modules/common/extract_genome_intervals/main.nf b/modules/common/extract_genome_intervals/main.nf
@@ -27,6 +27,9 @@ process extract_GenomeIntervals {
                pattern: ".command.*",
                saveAs: { "${task.process.replace(':', '/')}/log${file(it).getName()}" }
 
+    // This process uses the publishDir method to save the log files
+    ext capture_logs: false
+
     input:
     path(reference_dict)
 
@@ -42,4 +45,4 @@ process extract_GenomeIntervals {
     sed -e 's/SN://g' \
     > genomic_intervals.list
     """
-}
+}
diff --git a/modules/common/intermediate_file_removal/main.nf b/modules/common/intermediate_file_removal/main.nf
@@ -24,6 +24,9 @@ process remove_intermediate_files {
       mode: "copy",
       saveAs: { "${task.process.split(':')[-1]}/${task.process.split(':')[-1]}-${task.index}/log${file(it).getName()}" }
 
+    // This process uses the publishDir method to save the log files
+    ext capture_logs: false
+
     input:
     path(input_file_to_remove), stageAs: "delete.file"
     val(ready_for_deletion_signal)