diff --git a/tasks/utilities/data_export/task_export_two_tsvs.wdl b/tasks/utilities/data_export/task_export_two_tsvs.wdl index d3707441f..4410e29a8 100644 --- 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 index 40586fbf3..5e5f64468 100644 --- 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 index 5ab9247ad..4eb101b2e 100644 --- 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 index 638052ab0..22f95453a 100644 --- 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 >> output { diff --git a/tasks/utilities/file_handling/task_transfer_files.wdl b/tasks/utilities/file_handling/task_transfer_files.wdl index 28cfbebb9..1115df119 100644 --- 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 index 694b4f0e8..ab384c86b 100644 --- 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 index b33428777..aad099a4e 100644 --- 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 index 60a1a2fa0..6a7e2a86a 100644 --- 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