From 9e6e7307ff4ea3986c9b331937014d9abb6c0c89 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Mon, 12 Sep 2022 15:05:53 -0700 Subject: [PATCH] Apply suggestions from code review will squash in a moment Co-authored-by: Victor Lin <13424970+victorlin@users.noreply.github.com> Co-authored-by: Jover Lee --- docs/src/guides/run-analysis-on-terra.rst | 6 +++--- docs/src/guides/run-ingest-on-terra.rst | 20 ++++++++++---------- 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/docs/src/guides/run-analysis-on-terra.rst b/docs/src/guides/run-analysis-on-terra.rst index 0e36af77e..7146b5fb6 100644 --- a/docs/src/guides/run-analysis-on-terra.rst +++ b/docs/src/guides/run-analysis-on-terra.rst @@ -70,7 +70,7 @@ Connect your data files to the WDL workflow |Nextstrain_WRKFLW| sequence_fasta | File | this.sequences | +-----------------+------------------+-------+----------------------+ -10. If creating a build with multiple sequence and metadata files, can upload a targz folder containing the files. Otherwise skip +10. If creating a build with multiple sequence and metadata files, can upload a tarball containing the files. Otherwise skip +-----------------+-----------------+-------+----------------------+ |Task name | Variable | Type | Attribute | @@ -78,7 +78,7 @@ Connect your data files to the WDL workflow |Nextstrain_WRKFLW| context_targz | File | this.context_targz | +-----------------+-----------------+-------+----------------------+ -11. OPTIONAL CHANGE: If you are uploading gisaid/genbank, or very large sequence files, it is highly recommended to increase disk size. +11. OPTIONAL CHANGE: If you are uploading GISAID/GenBank, or very large sequence files, it is highly recommended to increase disk size. +-----------------+-------------------+-------+---------------------------------------------+ |Task name | Variable | Type | Description | @@ -91,7 +91,7 @@ Connect your data files to the WDL workflow +-----------------+-----------------------+--------+--------------------------------+ |Task name | Variable | Type | Description | +=================+=======================+========+================================+ - |Nextstrain_WRKFLW| s3deply | String | nextstrain provided url string | + |Nextstrain_WRKFLW| s3deploy | String | nextstrain provided url string | +-----------------+-----------------------+--------+--------------------------------+ |Nextstrain_WRKFLW| AWS_ACCESS_KEY_ID | String | your group access key id | +-----------------+-----------------------+--------+--------------------------------+ diff --git a/docs/src/guides/run-ingest-on-terra.rst b/docs/src/guides/run-ingest-on-terra.rst index 4bc4f777e..42c3bc9fc 100644 --- a/docs/src/guides/run-ingest-on-terra.rst +++ b/docs/src/guides/run-ingest-on-terra.rst @@ -1,22 +1,22 @@ -************************** -Run Data Ingest on Terra -************************** +******************************* +Ingest SARS-CoV-2 data on Terra +******************************* We have provided two pipelines for importing data into Terra: * GenBank Ingest - pull a public dataset and send them through our preprocessing scripts. -* GISAID Ingest - pull a private dataset if a user has their own API key, account, and password. +* GISAID Ingest - pull a private dataset if a user has their own API endpoint, username, and password. -The pipelines were mainly motivated to provide access to our data pre-processing scripts. Currently, these are focused on pulling datasets for the ncov workflow and is roughly diagramed below: +The pipelines were mainly motivated to provide access to our data pre-processing scripts. Currently, these are focused on pulling datasets for the ncov workflow and is roughly diagrammed below: .. image:: ../images/terra-ingest.png -Import ``ingest`` wdl workflow from Dockstore +Import the wdl workflow from Dockstore ============================================= 1. `Setup a Terra account `_ -#. Navigate to Dockstore: `ncov:wdl/genbank_ingest`_ or `ncov:wdl/gisaid_ingest`_ depending on if you wish to pull open (genbank) data or private (and have an gisaid api key) data. +#. Navigate to Dockstore: `ncov:wdl/genbank_ingest`_ or `ncov:wdl/gisaid_ingest`_ depending on if you wish to pull open (GenBank) data or private (and have an GISAID API endpoint) data. #. Top right corner, under **Launch with**, click on **Terra** #. Under "Workflow Name" set a name, such as ``genbank_ingest`` or ``gisaid_ingest``, and select your "Destination Workspace" in the drop down menu. #. Click button **IMPORT** @@ -25,8 +25,8 @@ Import ``ingest`` wdl workflow from Dockstore .. _`ncov:wdl/genbank_ingest`: https://dockstore.org/workflows/github.com/nextstrain/ncov:wdl/genbank_ingest?tab=info .. _`ncov:wdl/gisaid_ingest`: https://dockstore.org/workflows/github.com/nextstrain/ncov:wdl/gisaid_ingest?tab=info -Create Terra Variables for GISAID API -===================================== +Create Terra Variables for GISAID API Endpoint +================================================ If you are pulling GISAID data you must have your own API key. If you are pulling GenBank data (open), click on your imported "genbank_ingest" and skip to step 6. @@ -37,7 +37,7 @@ If you are pulling GISAID data you must have your own API key. If you are pullin +-----------------------------+----------------------------+-----------------------------------------------+ |Key | Value | Description | +=============================+============================+===============================================+ - |GISAID_API_ENDPOINT | url api enpoint value here | Provided by GISAID for your account | + |GISAID_API_ENDPOINT |URL API endpoint value here | Provided by GISAID for your account | +-----------------------------+----------------------------+-----------------------------------------------+ |GISAID_USERNAME_AND_PASSWORD | username:password | Your GISAID username password for api access | +-----------------------------+----------------------------+-----------------------------------------------+