Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[Mercury] prevent silent failures #648

Merged
merged 2 commits into from
Oct 17, 2024
Merged

[Mercury] prevent silent failures #648

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
27f7f12
prevent silent failures
sage-wright Oct 15, 2024
a6f80d9
add clarifying text
sage-wright Oct 15, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 6 additions & 3 deletions docs/workflows/public_data_sharing/mercury_prep_n_batch.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -52,22 +52,25 @@ 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"` |
| `assembly_mean_coverage_column_name` | `"assembly_mean_coverage"` | `"clearlabs_assembly_coverage"` | `"assembly_mean_coverage"` | `"clearlabs_assembly_coverage"` |

### 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 |
Expand Down
3 changes: 3 additions & 0 deletions tasks/utilities/submission/task_mercury.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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 \
Expand Down