From 873871fc887440838de9c96b49ea46b6d87020f7 Mon Sep 17 00:00:00 2001 From: Chenying Zhao Date: Tue, 25 Jul 2023 11:46:42 -0400 Subject: [PATCH] change example yaml sections to code block of yaml --- docs/source/preparation_config_yaml_file.rst | 24 +++++++++++++++----- 1 file changed, 18 insertions(+), 6 deletions(-) diff --git a/docs/source/preparation_config_yaml_file.rst b/docs/source/preparation_config_yaml_file.rst index a7c3347b..49edaf18 100644 --- a/docs/source/preparation_config_yaml_file.rst +++ b/docs/source/preparation_config_yaml_file.rst @@ -77,7 +77,9 @@ Instead, users are expected to define these in this section, **singularity_run** Example **singularity_run** ----------------------------------- -Below is example section **singularity_run** for ``fMRIPrep``:: +Below is example section **singularity_run** for ``fMRIPrep``: + +.. code-block:: yaml singularity_run: -w: "$BABS_TMPDIR" # this is a placeholder for temporary workspace @@ -507,7 +509,9 @@ and the interpreting shell for executing the job script. Example section **cluster_resources** ---------------------------------------- -Example section **cluster_resources** for ``QSIPrep``:: +Example section **cluster_resources** for ``QSIPrep``: + +.. code-block:: yaml cluster_resources: interpreting_shell: /bin/bash @@ -647,7 +651,9 @@ bash commands that are required by job running. An example would be to activate however, different clusters may require different commands to do so. Therefore, BABS asks the user to provide it. -Example section **script_preamble** for a specific cluster:: +Example section **script_preamble** for a specific cluster: + +.. code-block:: yaml script_preamble: | source ${CONDA_PREFIX}/bin/activate babs # Penn Med CUBIC cluster; replace 'babs' with your conda env name @@ -692,7 +698,9 @@ to (saved in) the output RIA (i.e., a permanent storage) where your BABS project We recommend using space that automatically cleans after the job finishes especially for large-scale dataset which has a large amount of jobs to do. -Example section **job_compute_space**:: +Example section **job_compute_space**: + +.. code-block:: yaml job_compute_space: "${CBICA_TMPDIR}" # Penn Med CUBIC cluster tmp space @@ -733,7 +741,9 @@ You may have a dataset where not all the subjects (and sessions) have the requir running the BIDS App. You can simply provide this list of required files, and BABS will exclude those subjects and sessions who don't have any of listed required files. -Example section **required_files** for ``fMRIPrep``:: +Example section **required_files** for ``fMRIPrep``: + +.. code-block:: yaml required_files: $INPUT_DATASET_#1: @@ -777,7 +787,9 @@ This section is optional. This section is to define a list of alert messages to be searched in log files, and these messages may indicates failure of a job. -Example section **alert_log_messages** for fMRIPrep:: +Example section **alert_log_messages** for fMRIPrep: + +.. code-block:: yaml alert_log_messages: stdout: