diff --git a/docs/workflows/public_data_sharing/mercury_prep_n_batch.md b/docs/workflows/public_data_sharing/mercury_prep_n_batch.md index 77efad884..5126e24bb 100644 --- a/docs/workflows/public_data_sharing/mercury_prep_n_batch.md +++ b/docs/workflows/public_data_sharing/mercury_prep_n_batch.md @@ -52,7 +52,7 @@ To help users collect all required metadata, we have created the following Excel The `using_clearlabs_data` and `using_reads_dehosted` arguments change the default values for the `read1_column_name`, `assembly_fasta_column_name`, and `assembly_mean_coverage_column_name` metadata columns. The default values are shown in the table below in addition to what they are changed to depending on what arguments are used. - | Variable | Default Value | with `using_clearlabs_data` | with `using_reads_dehosted` | with both  `using_clearlabs_data` ***and*** `using_reads_dehosted` | + | Variable | Default Value | with `using_clearlabs_data` | with `using_reads_dehosted` | with both  `using_clearlabs_data` **_and_** `using_reads_dehosted` | | --- | --- | --- | --- | --- | | `read1_column_name` | `"read1_dehosted"` | `"clearlabs_fastq_gz"` | `"reads_dehosted"` | `"reads_dehosted"` | | `assembly_fasta_column_name` | `"assembly_fasta"` | `"clearlabs_fasta"` | `"assembly_fasta"` | `"clearlabs_fasta"` | @@ -60,14 +60,17 @@ To help users collect all required metadata, we have created the following Excel ### Inputs +!!! tip "Use the sample table for the `terra_table_name` input" + Make sure your entry for `terra_table_name` is for the _sample_ table! While the root entity needs to be the set table, the input value for `terra_table_name` should be the sample table. + This workflow runs on the set-level. | **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** | |---|---|---|---|---|---| | mercury_prep_n_batch | **gcp_bucket_uri** | String | Google bucket where your SRA reads will be temporarily stored before transferring to SRA. Example: "gs://theiagen_sra_transfer" | | Required | | mercury_prep_n_batch | **sample_names** | Array[String] | The samples you want to submit | | Required | -| mercury_prep_n_batch | **terra_project_name** | String | The name of your Terra project. You can find this information in the URL of the webpage of your Terra dashboard. For example, if your URL contains #workspaces/example/my_workspace/ then your project name is example | | Required | -| mercury_prep_n_batch | **terra_table_name** | String | The name of the Terra table where your samples can be found. Do not include the entity: prefix or the _id suffix, just the name of the table as listed in the sidebar on lefthand side of the Terra Data tab. | | Required | +| mercury_prep_n_batch | **terra_project_name** | String | The name of your Terra project. You can find this information in the URL of the webpage of your Terra dashboard. For example, if your URL contains `#workspaces/example/my_workspace/` then your project name is `example` | | Required | +| mercury_prep_n_batch | **terra_table_name** | String | The name of the Terra table where your **samples** can be found. Do not include the `entity:` prefix, the `_id` suffix, or the `_set_id` suffix, just the name of the sample-level data table as listed in the sidebar on lefthand side of the Terra Data tab. | | Required | | mercury_prep_n_batch | **terra_workspace_name** | String | The name of your Terra workspace where your samples can be found. For example, if your URL contains #workspaces/example/my_workspace/ then your project name is my_workspace | | Required | | download_terra_table | **cpu** | Int | Number of CPUs to allocate to the task | 1 | Optional | | download_terra_table | **disk_size** | Int | Amount of storage (in GB) to allocate to the task | 10 | Optional | diff --git a/tasks/utilities/submission/task_mercury.wdl b/tasks/utilities/submission/task_mercury.wdl index 51ce839e1..d445e92aa 100644 --- a/tasks/utilities/submission/task_mercury.wdl +++ b/tasks/utilities/submission/task_mercury.wdl @@ -29,6 +29,9 @@ task mercury { volatile: true } command <<< + #set -euo pipefail to avoid silent failure + set -euo pipefail + python3 /mercury/mercury/mercury.py -v | tee VERSION python3 /mercury/mercury/mercury.py \