diff --git a/docs/index.rst b/docs/index.rst index d68ae690..361b1347 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -51,6 +51,7 @@ Contents install usage/index workflows/index + yaml_docs/index tutorials/index ../changelog contribute_guidelines diff --git a/docs/yaml_docs/index.rst b/docs/yaml_docs/index.rst new file mode 100644 index 00000000..165080a5 --- /dev/null +++ b/docs/yaml_docs/index.rst @@ -0,0 +1,10 @@ +Workflows configuration files +============================= + +.. toctree:: + :maxdepth: 1 + + pipeline_ingestion_yml + spatial_qc + spatial_preprocess + spatial_deconvolution \ No newline at end of file diff --git a/docs/yaml_docs/pipeline_ingestion_yml.md b/docs/yaml_docs/pipeline_ingestion_yml.md index 4afbff7c..c1ebed3a 100644 --- a/docs/yaml_docs/pipeline_ingestion_yml.md +++ b/docs/yaml_docs/pipeline_ingestion_yml.md @@ -8,7 +8,10 @@ } -# pipeline.yml for ingestion workflow +# Ingestion YAML + +In this documentation, the parameters of the `ingest` configuration yaml file are explained. +This file is generated running `panpipes ingest config`.
The individual steps run by the pipeline are described in the [spatial preprocess workflow](../workflows/qc.md). ## Compute resources options diff --git a/docs/yaml_docs/spatial_deconvolution.md b/docs/yaml_docs/spatial_deconvolution.md index 37b3b787..1e3fef01 100644 --- a/docs/yaml_docs/spatial_deconvolution.md +++ b/docs/yaml_docs/spatial_deconvolution.md @@ -1,7 +1,9 @@ # Spatial Deconvolution YAML -In this documentation, the parameters of the `deconvolution_spatial` yaml file are explained. In general, the user can leave parameters empty to use defaults.
The individual steps run by the pipeline are described in the [spatial deconvolution workflow](../workflows/deconvolute_spatial.md). +In this documentation, the parameters of the `deconvolution_spatial` yaml file are explained. +This file is generated running `panpipes deconvolution config`. +In general, the user can leave parameters empty to use defaults.
The individual steps run by the pipeline are described in the [spatial deconvolution workflow](../workflows/deconvolute_spatial.md). diff --git a/docs/yaml_docs/spatial_preprocess.md b/docs/yaml_docs/spatial_preprocess.md index 7bf9a948..b443d4e2 100644 --- a/docs/yaml_docs/spatial_preprocess.md +++ b/docs/yaml_docs/spatial_preprocess.md @@ -1,7 +1,8 @@ # Spatial Preprocessing YAML -In this documentation, the parameters of the `preprocess_spatial` yaml file are explained. In general, the user can leave parameters empty to use defaults.
The individual steps run by the pipeline are described in the [spatial preprocess workflow](../workflows/preprocess_spatial.md). +In this documentation, the parameters of the `preprocess_spatial` yaml file are explained. +This file is generated running `panpipes preprocess_spatial config`. In general, the user can leave parameters empty to use defaults.
The individual steps run by the pipeline are described in the [spatial preprocess workflow](../workflows/preprocess_spatial.md). diff --git a/docs/yaml_docs/spatial_qc.md b/docs/yaml_docs/spatial_qc.md index 2c31f39e..6c933d7f 100644 --- a/docs/yaml_docs/spatial_qc.md +++ b/docs/yaml_docs/spatial_qc.md @@ -1,7 +1,9 @@ # Spatial QC YAML -In this documentation, the parameters of the `qc_spatial` yaml file are explained. In general, the user can leave parameters empty to use defaults.
The individual steps run by the pipeline are described in the [spatial QC workflow](../workflows/ingest_spatial.md). +In this documentation, the parameters of the `qc_spatial` yaml file are explained. +This file is generated running `panpipes qc_spatial config`. +In general, the user can leave parameters empty to use defaults.
The individual steps run by the pipeline are described in the [spatial QC workflow](../workflows/ingest_spatial.md).