Prevent Silent Errors (#666)

* tada * two more * update
theiagen · Nov 8, 2024 · 2669f99 · 2669f99
1 parent 2fd9f75
commit 2669f99
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Showing 8 changed files with 15 additions and 2 deletions.
diff --git a/tasks/utilities/data_export/task_export_two_tsvs.wdl b/tasks/utilities/data_export/task_export_two_tsvs.wdl
@@ -18,6 +18,7 @@ task export_two_tsvs {
     volatile: true
   }
   command <<<
+    set -euo pipefail
     python3 /scripts/export_large_tsv/export_large_tsv.py --project ~{terra_project1} --workspace ~{terra_workspace1} --entity_type ~{datatable1} --tsv_filename "~{datatable1}_table1.tsv"
 
     # check if second project is provided; if not, use first

diff --git a/tasks/utilities/data_handling/task_summarize_data.wdl b/tasks/utilities/data_handling/task_summarize_data.wdl
@@ -23,6 +23,8 @@ task summarize_data {
     volatile: true
   }
   command <<<   
+    set -euo pipefail
+
     # when running on terra, comment out all input_table mentions
     python3 /scripts/export_large_tsv/export_large_tsv.py --project "~{terra_project}" --workspace "~{terra_workspace}" --entity_type ~{terra_table} --tsv_filename ~{terra_table}-data.tsv 
 

diff --git a/tasks/utilities/data_handling/task_theiacov_fasta_batch.wdl b/tasks/utilities/data_handling/task_theiacov_fasta_batch.wdl
@@ -28,6 +28,8 @@ task sm_theiacov_fasta_wrangling { # the sm stands for supermassive
     Int memory = 4
   }
   command <<<
+    set -euo pipefail
+
     # check if nextclade json file exists
     if [ -f ~{nextclade_json} ]; then
       # this line splits into individual json files

diff --git a/tasks/utilities/data_import/task_create_terra_table.wdl b/tasks/utilities/data_import/task_create_terra_table.wdl
@@ -146,6 +146,10 @@ task create_terra_table {
     done <filelist-fullpath.txt
 
     echo "DEBUG: terra table created, now beginning upload"
+
+    # set error handling to exit if the subsequent import_large_tsv.py task fails
+    set -euo pipefail
+
     python3 /scripts/import_large_tsv/import_large_tsv.py --project "~{terra_project}" --workspace "~{terra_workspace}" --tsv terra_table_to_upload.tsv
   >>>
   output {

diff --git a/tasks/utilities/file_handling/task_transfer_files.wdl b/tasks/utilities/file_handling/task_transfer_files.wdl
@@ -14,6 +14,8 @@ task transfer_files {
     volatile: true
   }
   command <<<
+    set -euo pipefail
+
     file_path_array="~{sep=' ' files_to_transfer}"
 
     gsutil -m cp -n ${file_path_array[@]} ~{target_bucket}

diff --git a/tasks/utilities/submission/task_submission.wdl b/tasks/utilities/submission/task_submission.wdl
@@ -23,6 +23,8 @@ task prune_table {
     volatile: true
   }
   command <<<
+    set -euo pipefail
+
     # when running on terra, comment out all input_table mentions
     python3 /scripts/export_large_tsv/export_large_tsv.py --project "~{project_name}" --workspace "~{workspace_name}" --entity_type ~{table_name} --tsv_filename ~{table_name}-data.tsv
 

diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
@@ -627,7 +627,7 @@
     - path: miniwdl_run/wdl/tasks/taxon_id/contamination/task_midas.wdl
       md5sum: 64caaaff5910ac0036e2659434500962
     - path: miniwdl_run/wdl/tasks/utilities/data_export/task_broad_terra_tools.wdl
-      md5sum: 8c97c5bd65e2787239f12ef425d479ae
+      md5sum: 850ad97598aca5c28eb36e6a5c13c2fc
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
       md5sum: d8db687487a45536d4837a540ed2a135
     - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl

diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
@@ -590,7 +590,7 @@
     - path: miniwdl_run/wdl/tasks/taxon_id/contamination/task_midas.wdl
       md5sum: 64caaaff5910ac0036e2659434500962
     - path: miniwdl_run/wdl/tasks/utilities/data_export/task_broad_terra_tools.wdl
-      md5sum: 8c97c5bd65e2787239f12ef425d479ae
+      md5sum: 850ad97598aca5c28eb36e6a5c13c2fc
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_se.wdl
       md5sum: 4111a758490174325ae8ea52a95319e9
     - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl