Disable archiving to object storage

LEEF-UZH · Oct 3, 2022 · 123bdb1 · 123bdb1
1 parent be12e53
commit 123bdb1
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Showing 5 changed files with 148 additions and 128 deletions.
diff --git a/pipeline/run.pipeline.bemovi b/pipeline/run.pipeline.bemovi
@@ -40,16 +40,17 @@ LEEF::init_LEEF(config_file = pipeline, id = argv[[1]])
 
 LEEF::process(process = FALSE)
 
-message("\n########################################################\n")
+# message("\n########################################################\n")
 message("\narchiving raw data ...\n")
-LEEF.archive.default::run_archive_none_subdir(
-  input = getOption("LEEF")$directories$raw,
-  output = file.path(getOption("LEEF")$directories$archive, "raw")
-)
-LEEF.archive.default::run_archive_none(
-  input = getOption("LEEF")$directories$general.parameter,
-  output = file.path(getOption("LEEF")$directories$archive, "raw")
-)
+message("\nDISABLED\n")
+# LEEF.archive.default::run_archive_none_subdir(
+#   input = getOption("LEEF")$directories$raw,
+#   output = file.path(getOption("LEEF")$directories$archive, "raw")
+# )
+# LEEF.archive.default::run_archive_none(
+#   input = getOption("LEEF")$directories$general.parameter,
+#   output = file.path(getOption("LEEF")$directories$archive, "raw")
+# )
 message("done\n")
 message("\n########################################################\n")
 
@@ -61,11 +62,12 @@ message("\n########################################################\n")
 
 message("\n########################################################\n")
 message("\narchiving pre-processed data...\n")
-LEEF.archive.default::run_archive_none_subdir(
-  input = getOption("LEEF")$directories$pre_processed,
-  output = file.path(getOption("LEEF")$directories$archive, "pre_processed")
-)
-message("done\n")
+message("\nDISABLED\n")
+# LEEF.archive.default::run_archive_none_subdir(
+#   input = getOption("LEEF")$directories$pre_processed,
+#   output = file.path(getOption("LEEF")$directories$archive, "pre_processed")
+# )
+# message("done\n")
 message("\n########################################################\n")
 
 message("\n########################################################\n")
@@ -76,11 +78,12 @@ message("\n########################################################\n")
 
 message("\n########################################################\n")
 message("\narchiving extracted data ...\n")
-LEEF.archive.default::run_archive_none_subdir(
-  input = getOption("LEEF")$directories$extracted,
-  output = file.path(getOption("LEEF")$directories$archive, "extracted")
-)
-message("done\n")
+message("\nDISABLED\n")
+# LEEF.archive.default::run_archive_none_subdir(
+#   input = getOption("LEEF")$directories$extracted,
+#   output = file.path(getOption("LEEF")$directories$archive, "extracted")
+# )
+# message("done\n")
 message("\n########################################################\n")
 
 message("\n########################################################\n")
@@ -95,9 +98,10 @@ message("\n########################################################\n")
 
 message("\n########################################################\n")
 message("\narchiving backend ...\n")
-LEEF.archive.default::run_archive_none(
-  input = getOption("LEEF")$directories$backend,
-  output = file.path(getOption("LEEF")$directories$archive, "backend")
-)
-message("done\n")
+message("\nDISABLED\n")
+# LEEF.archive.default::run_archive_none(
+#   input = getOption("LEEF")$directories$backend,
+#   output = file.path(getOption("LEEF")$directories$archive, "backend")
+# )
+# message("done\n")
 message("\n########################################################\n")
diff --git a/pipeline/run.pipeline.flowcam b/pipeline/run.pipeline.flowcam
@@ -34,15 +34,16 @@ LEEF::process(process = FALSE)
 
 message("\n########################################################\n")
 message("\narchiving raw data ...\n")
-LEEF.archive.default::run_archive_none_subdir(
-  input = getOption("LEEF")$directories$raw,
-  output = file.path(getOption("LEEF")$directories$archive, "raw")
-)
-LEEF.archive.default::run_archive_none(
-  input = getOption("LEEF")$directories$general.parameter,
-  output = file.path(getOption("LEEF")$directories$archive, "raw")
-)
-message("done\n")
+message("\nDISABLED\n")
+# LEEF.archive.default::run_archive_none_subdir(
+#   input = getOption("LEEF")$directories$raw,
+#   output = file.path(getOption("LEEF")$directories$archive, "raw")
+# )
+# LEEF.archive.default::run_archive_none(
+#   input = getOption("LEEF")$directories$general.parameter,
+#   output = file.path(getOption("LEEF")$directories$archive, "raw")
+# )
+# message("done\n")
 message("\n########################################################\n")
 
 message("\n########################################################\n")
@@ -53,11 +54,12 @@ message("\n########################################################\n")
 
 message("\n########################################################\n")
 message("\narchiving pre-processed data...\n")
-LEEF.archive.default::run_archive_none_subdir(
-  input = getOption("LEEF")$directories$pre_processed,
-  output = file.path(getOption("LEEF")$directories$archive, "pre_processed")
-)
-message("done\n")
+message("\nDISABLED\n")
+# LEEF.archive.default::run_archive_none_subdir(
+#   input = getOption("LEEF")$directories$pre_processed,
+#   output = file.path(getOption("LEEF")$directories$archive, "pre_processed")
+# )
+# message("done\n")
 message("\n########################################################\n")
 
 message("\n########################################################\n")
@@ -68,13 +70,14 @@ message("\n########################################################\n")
 
 message("\n########################################################\n")
 message("\narchiving extracted data ...\n")
-message("     ", getOption("LEEF")$directories$extracted)
-message("     ", file.path(getOption("LEEF")$directories$archive, "extracted"))
-LEEF.archive.default::run_archive_none_subdir(
-  input = getOption("LEEF")$directories$extracted,
-  output = file.path(getOption("LEEF")$directories$archive, "extracted")
-)
-message("done\n")
+message("\nDISABLED\n")
+# message("     ", getOption("LEEF")$directories$extracted)
+# message("     ", file.path(getOption("LEEF")$directories$archive, "extracted"))
+# LEEF.archive.default::run_archive_none_subdir(
+#   input = getOption("LEEF")$directories$extracted,
+#   output = file.path(getOption("LEEF")$directories$archive, "extracted")
+# )
+# message("done\n")
 message("\n########################################################\n")
 
 
@@ -86,9 +89,10 @@ message("\n########################################################\n")
 
 message("\n########################################################\n")
 message("\narchiving backend ...\n")
-LEEF.archive.default::run_archive_none(
-  input = getOption("LEEF")$directories$backend,
-  output = file.path(getOption("LEEF")$directories$archive, "backend_fast_only")
-)
-message("done\n")
+message("\nDISABLED\n")
+# LEEF.archive.default::run_archive_none(
+#   input = getOption("LEEF")$directories$backend,
+#   output = file.path(getOption("LEEF")$directories$archive, "backend_fast_only")
+# )
+# message("done\n")
 message("\n########################################################\n")
diff --git a/pipeline/run.pipeline.flowcytometer b/pipeline/run.pipeline.flowcytometer
@@ -34,15 +34,16 @@ LEEF::process(process = FALSE)
 
 message("\n########################################################\n")
 message("\narchiving raw data ...\n")
-LEEF.archive.default::run_archive_none_subdir(
-  input = getOption("LEEF")$directories$raw,
-  output = file.path(getOption("LEEF")$directories$archive, "raw")
-)
-LEEF.archive.default::run_archive_none(
-  input = getOption("LEEF")$directories$general.parameter,
-  output = file.path(getOption("LEEF")$directories$archive, "raw")
-)
-message("done\n")
+message("\nDISABLED\n")
+# LEEF.archive.default::run_archive_none_subdir(
+#   input = getOption("LEEF")$directories$raw,
+#   output = file.path(getOption("LEEF")$directories$archive, "raw")
+# )
+# LEEF.archive.default::run_archive_none(
+#   input = getOption("LEEF")$directories$general.parameter,
+#   output = file.path(getOption("LEEF")$directories$archive, "raw")
+# )
+# message("done\n")
 message("\n########################################################\n")
 
 message("\n########################################################\n")
@@ -53,11 +54,12 @@ message("\n########################################################\n")
 
 message("\n########################################################\n")
 message("\narchiving pre-processed data...\n")
-LEEF.archive.default::run_archive_none_subdir(
-  input = getOption("LEEF")$directories$pre_processed,
-  output = file.path(getOption("LEEF")$directories$archive, "pre_processed")
-)
-message("done\n")
+message("\nDISABLED\n")
+# LEEF.archive.default::run_archive_none_subdir(
+#   input = getOption("LEEF")$directories$pre_processed,
+#   output = file.path(getOption("LEEF")$directories$archive, "pre_processed")
+# )
+# message("done\n")
 message("\n########################################################\n")
 
 message("\n########################################################\n")
@@ -68,13 +70,14 @@ message("\n########################################################\n")
 
 message("\n########################################################\n")
 message("\narchiving extracted data ...\n")
-message("     ", getOption("LEEF")$directories$extracted)
-message("     ", file.path(getOption("LEEF")$directories$archive, "extracted"))
-LEEF.archive.default::run_archive_none_subdir(
-  input = getOption("LEEF")$directories$extracted,
-  output = file.path(getOption("LEEF")$directories$archive, "extracted")
-)
-message("done\n")
+message("\nDISABLED\n")
+# message("     ", getOption("LEEF")$directories$extracted)
+# message("     ", file.path(getOption("LEEF")$directories$archive, "extracted"))
+# LEEF.archive.default::run_archive_none_subdir(
+#   input = getOption("LEEF")$directories$extracted,
+#   output = file.path(getOption("LEEF")$directories$archive, "extracted")
+# )
+# message("done\n")
 message("\n########################################################\n")
 
 
@@ -86,9 +89,10 @@ message("\n########################################################\n")
 
 message("\n########################################################\n")
 message("\narchiving backend ...\n")
-LEEF.archive.default::run_archive_none(
-  input = getOption("LEEF")$directories$backend,
-  output = file.path(getOption("LEEF")$directories$archive, "backend_fast_only")
-)
-message("done\n")
+message("\nDISABLED\n")
+# LEEF.archive.default::run_archive_none(
+#   input = getOption("LEEF")$directories$backend,
+#   output = file.path(getOption("LEEF")$directories$archive, "backend_fast_only")
+# )
+# message("done\n")
 message("\n########################################################\n")
diff --git a/pipeline/run.pipeline.manualcount b/pipeline/run.pipeline.manualcount
@@ -34,15 +34,16 @@ LEEF::process(process = FALSE)
 
 message("\n########################################################\n")
 message("\narchiving raw data ...\n")
-LEEF.archive.default::run_archive_none_subdir(
-  input = getOption("LEEF")$directories$raw,
-  output = file.path(getOption("LEEF")$directories$archive, "raw")
-)
-LEEF.archive.default::run_archive_none(
-  input = getOption("LEEF")$directories$general.parameter,
-  output = file.path(getOption("LEEF")$directories$archive, "raw")
-)
-message("done\n")
+message("\nDISABLED\n")
+# LEEF.archive.default::run_archive_none_subdir(
+#   input = getOption("LEEF")$directories$raw,
+#   output = file.path(getOption("LEEF")$directories$archive, "raw")
+# )
+# LEEF.archive.default::run_archive_none(
+#   input = getOption("LEEF")$directories$general.parameter,
+#   output = file.path(getOption("LEEF")$directories$archive, "raw")
+# )
+# message("done\n")
 message("\n########################################################\n")
 
 message("\n########################################################\n")
@@ -53,11 +54,12 @@ message("\n########################################################\n")
 
 message("\n########################################################\n")
 message("\narchiving pre-processed data...\n")
-LEEF.archive.default::run_archive_none_subdir(
-  input = getOption("LEEF")$directories$pre_processed,
-  output = file.path(getOption("LEEF")$directories$archive, "pre_processed")
-)
-message("done\n")
+message("\nDISABLED\n")
+# LEEF.archive.default::run_archive_none_subdir(
+#   input = getOption("LEEF")$directories$pre_processed,
+#   output = file.path(getOption("LEEF")$directories$archive, "pre_processed")
+# )
+# message("done\n")
 message("\n########################################################\n")
 
 message("\n########################################################\n")
@@ -68,13 +70,14 @@ message("\n########################################################\n")
 
 message("\n########################################################\n")
 message("\narchiving extracted data ...\n")
-message("     ", getOption("LEEF")$directories$extracted)
-message("     ", file.path(getOption("LEEF")$directories$archive, "extracted"))
-LEEF.archive.default::run_archive_none_subdir(
-  input = getOption("LEEF")$directories$extracted,
-  output = file.path(getOption("LEEF")$directories$archive, "extracted")
-)
-message("done\n")
+message("\nDISABLED\n")
+# message("     ", getOption("LEEF")$directories$extracted)
+# message("     ", file.path(getOption("LEEF")$directories$archive, "extracted"))
+# LEEF.archive.default::run_archive_none_subdir(
+#   input = getOption("LEEF")$directories$extracted,
+#   output = file.path(getOption("LEEF")$directories$archive, "extracted")
+# )
+# message("done\n")
 message("\n########################################################\n")
 
 
@@ -86,9 +89,10 @@ message("\n########################################################\n")
 
 message("\n########################################################\n")
 message("\narchiving backend ...\n")
-LEEF.archive.default::run_archive_none(
-  input = getOption("LEEF")$directories$backend,
-  output = file.path(getOption("LEEF")$directories$archive, "backend_fast_only")
-)
-message("done\n")
+message("\nDISABLED\n")
+# LEEF.archive.default::run_archive_none(
+#   input = getOption("LEEF")$directories$backend,
+#   output = file.path(getOption("LEEF")$directories$archive, "backend_fast_only")
+# )
+# message("done\n")
 message("\n########################################################\n")