Doc updates

- typo fixes, edit for clarity

README.rst

@@ -8,7 +8,8 @@ A repository of pipelines for single-cell data analysis in Nextflow DSL2.
 
 **Full documentation** is available on `Read the Docs <https://vsn-pipelines.readthedocs.io/en/latest/>`_, or take a look at the `Quick Start <https://vsn-pipelines.readthedocs.io/en/latest/getting-started.html#quick-start>`_ guide.
 
-This main repo contains multiple workflows for analyzing single cell transcriptomics data, and depends on a number of tools, which are organized into submodules within the VIB-Singlecell-NF_ organization.
+This main repo contains multiple workflows for analyzing single cell transcriptomics data, and depends on a number of tools, which are organized into subfolders within the ``src/`` directory.
+The VIB-Singlecell-NF_ organization contains this main repo along with a collection of example runs (`VSN-Pipelines-examples <https://vsn-pipelines-examples.readthedocs.io/en/latest/>`_).
 Currently available workflows are listed below.
 
 If VSN-Pipelines is useful for your research, consider citing:
@@ -109,6 +110,7 @@ Sample Aggregation Workflows
 
 
 ---
+
 In addition, the pySCENIC_ implementation of the SCENIC_ workflow is integrated here and can be run in conjunction with any of the above workflows.
 The output of each of the main workflows is a loom_-format file, which is ready for import into the interactive single-cell web visualization tool SCope_.
 In addition, data is also output in h5ad format, and reports are generated for the major pipeline steps.

docs/development.rst

@@ -83,7 +83,7 @@ Steps:
 
 #. Update the ``nextflow.config`` file to create the ``harmony.config`` configuration file.
 
-    * Each process's options should be in their own level. With a single proccess, you do not need one extra level.
+    * Each process's options should be in their own level. With a single process, you do not need one extra level.
 
     .. code:: dockerfile
 
@@ -624,7 +624,7 @@ Steps:
 
         }
 
-#. Finally add a new entry in main.nf of the ``vsn-pipelines`` repository
+#. Finally add a new entry in ``main.nf`` of the ``vsn-pipelines`` repository
 
     .. code:: groovy
 

docs/features.rst

@@ -55,14 +55,14 @@ Finally run the pipeline,
 
 Set the seed
 ------------
-Some steps in the pipelines are nondeterministic. In order to have reproducible results, a seed is set by default to:
+Some steps in the pipelines are non-deterministic. In order to have reproducible results, a seed is set by default to:
 
 .. code:: groovy
 
     workflow.manifest.version.replaceAll("\\.","").toInteger()
 
-The seed is a number derived from the the version of the pipeline used at the time of the analysis run.
-To override the seed (integer) you have edit the nextflow.config file with:
+The seed is a number derived from the version of the pipeline used at the time of the analysis run.
+To override the seed (integer) you have edit the ``nextflow.config`` file with:
 
 .. code:: groovy
 
@@ -154,19 +154,19 @@ Two methods (``params.sc.cell_annotate.method``) are available:
 
 If you have a single file containing the metadata information of all your samples, use ``aio`` method otherwise use ``obo``.
 
-For both methods, here are the mandatory params to set:
+For both methods, here are the mandatory parameters to set:
 
 - ``off`` should be set to ``h5ad``
 - ``method`` choose either ``obo`` or ``aio``
 - ``annotationColumnNames`` is an array of columns names from ``cellMetaDataFilePath`` containing different annotation metadata to add.
 
-If ``aio`` used, the following additional params are required:
+If ``aio`` used, the following additional parameters are required:
 
 - ``cellMetaDataFilePath`` is a file path pointing to a single .tsv file (with header) with at least 2 columns: a column containing all the cell IDs and an annotation column.
 - ``indexColumnName`` is the column name from ``cellMetaDataFilePath`` containing the cell IDs information. This column **can** have unique values; if it's not the case, it's important that the combination of the values from the ``indexColumnName`` and the ``sampleColumnName`` are unique. 
-- ``sampleColumnName`` is the column name from ``cellMetaDataFilePath`` containing the sample ID/name information. Make sur that the values from this column match the samples IDs inferred from the data files. To know how those are inferred, please read the `Input Data Formats`_ section.
+- ``sampleColumnName`` is the column name from ``cellMetaDataFilePath`` containing the sample ID/name information. Make sure that the values from this column match the samples IDs inferred from the data files. To know how those are inferred, please read the `Input Data Formats`_ section.
 
-If ``obo`` is used, the following params are required:
+If ``obo`` is used, the following parameters are required:
 
 - ``cellMetaDataFilePath``
 
@@ -267,7 +267,7 @@ Two methods (``params.sc.cell_filter.method``) are available:
 
 If you have a single file containing the metadata information of all your samples, use ``external`` method otherwise use ``internal``.
 
-For both methods, here are the mandatory params to set:
+For both methods, here are the mandatory parameters to set:
 
 - ``off`` should be set to ``h5ad``
 - ``method`` choose either ``internal`` or ``external``
@@ -276,20 +276,20 @@ For both methods, here are the mandatory params to set:
   - ``id`` is a short identifier for the filter
   - ``valuesToKeepFromFilterColumn`` is array of values from the ``filterColumnName`` that should be kept (other values will be filtered out).
 
-If ``internal`` used, the following additional params are required:
+If ``internal`` used, the following additional parameters are required:
 
 - ``filters`` is a List of Maps where each Map is required to have the following parameters:
 
   - ``sampleColumnName`` is the column name containing the sample ID/name information. It should exist in the ``obs`` column attribute of the h5ad.
   - ``filterColumnName`` is the column name that will be used to filter out cells.  It should exist in the ``obs`` column attribute of the h5ad.
 
-If ``external`` used, the following additional params are required:
+If ``external`` used, the following additional parameters are required:
 
 - ``filters`` is a List of Maps where each Map is required to have the following parameters:
 
   - ``cellMetaDataFilePath`` is a file path pointing to a single .tsv file (with header) with at least 3 columns: a column containing all the cell IDs, another containing the sample ID/name information, and a column to use for the filtering.
   - ``indexColumnName`` is the column name from ``cellMetaDataFilePath`` containing the cell IDs information. This column **must** have unique values. 
-  - `optional` ``sampleColumnName`` is the column name from ``cellMetaDataFilePath`` containing the sample ID/name information. Make sur that the values from this column match the samples IDs inferred from the data files. To know how those are inferred, please read the `Input Data Formats`_ section.
+  - `optional` ``sampleColumnName`` is the column name from ``cellMetaDataFilePath`` containing the sample ID/name information. Make sure that the values from this column match the samples IDs inferred from the data files. To know how those are inferred, please read the `Input Data Formats`_ section.
   - `optional` ``filterColumnName`` is the column name from ``cellMetaDataFilePath`` which be used to filter out cells.
 
 
@@ -348,8 +348,8 @@ If you want to apply custom parameters for some specific samples and have a "gen
         }
     }
 
-Using this config, the param ``params.sc.scanpy.cellFilterMinNGenes`` will be applied with a threshold value of ``600`` to ``1k_pbmc_v2_chemistry``.  The rest of the samples will use the value ``800`` to filter the cells having less than that number of genes.
-This strategy can be applied to any other paramameter of the config.
+Using this config, the parameter ``params.sc.scanpy.cellFilterMinNGenes`` will be applied with a threshold value of ``600`` to ``1k_pbmc_v2_chemistry``.  The rest of the samples will use the value ``800`` to filter the cells having less than that number of genes.
+This strategy can be applied to any other parameter of the config.
 
 
 Parameter exploration
@@ -437,4 +437,4 @@ The following command, will create a Nextflow config which the pipeline will und
        -profile min,[data-profile],scanpy_data_transformation,scanpy_normalization,[...],singularity > nextflow.config
 
 - ``[data-profile]``: Can be one of the different possible data profiles e.g.: ``h5ad``
-- ``[...]``: Can be other profiles like ``bbknn``, ``harmony``, ``pcacv``, ...
+- ``[...]``: Can be other profiles like ``bbknn``, ``harmony``, ``pcacv``, ...

docs/getting-started.rst

@@ -126,6 +126,6 @@ The pipelines will generate 3 types of results in the output directory (`params.
 
     - See the example output report from the 1k PBMC data `here <http://htmlpreview.github.io/?https://github.com/vib-singlecell-nf/vsn-pipelines/blob/master/notebooks/10x_PBMC.merged_report.html>`_
 
-- ``pipeline_reports``: nextflow dag, execution, timeline, and trace reports
+- ``pipeline_reports``: Nextflow dag, execution, timeline, and trace reports
 
 If you would like to use the pipelines on a custom dataset, please see the `pipelines <./pipelines.html>`_ section below.

docs/pipelines.rst

@@ -8,7 +8,7 @@ This pipeline can be configured and run on custom data with a few steps.
 The recommended method is to first run ``nextflow config ...`` to generate a complete config file (with the default parameters) in your working directory.
 The tool-specific parameters, as well as Docker/Singularity profiles, are included when specifying the appropriate profiles to ``nextflow config``.
 
-1. First, update to the latest pipeline version (this will update the nextflow cache of the repository, typically located in ``~/.nextflow/assets/vib-singlecell-nf/``)::
+1. First, update to the latest pipeline version (this will update the Nextflow cache of the repository, typically located in ``~/.nextflow/assets/vib-singlecell-nf/``)::
 
     nextflow pull vib-singlecell-nf/vsn-pipelines
 
@@ -502,14 +502,14 @@ The output is a loom file with the results embedded.
 Utility Pipelines
 *****************
 
-Contrary to the aformentioned pipelines, these are not end-to-end. They are used to perfom small incremental processing steps.
+Contrary to the aformentioned pipelines, these are not end-to-end. They are used to perform small incremental processing steps.
 
 **cell_annotate**
 -----------------
 
 Runs the ``cell_annotate`` workflow which will perform a cell-based annotation of the data using a set of provided .tsv metadata files.
 We show a use case here below with 10x Genomics data were it will annotate different samples using the ``obo`` method. For more information
-about this cell-based annotation feautre please visit `Cell-based metadata annotation`_ section.
+about this cell-based annotation feature please visit `Cell-based metadata annotation`_ section.
 
 .. _`Cell-based metadata annotation`: https://vsn-pipelines.readthedocs.io/en/latest/features.html#cell-based-metadata-annotation
 
@@ -561,7 +561,7 @@ Now we can run it with the following command:
 
 Runs the ``cell_annotate_filter`` workflow which will perform a cell-based annotation of the data using a set of provided .tsv metadata files following by a cell-based filtering.
 We show a use case here below with 10x Genomics data were it will annotate different samples using the ``obo`` method. For more information
-about this cell-based annotation feautre please visit `Cell-based metadata annotation`_ section and `Cell-based metadata filtering`_ section.
+about this cell-based annotation feature please visit `Cell-based metadata annotation`_ section and `Cell-based metadata filtering`_ section.
 
 .. _`Cell-based metadata filtering`: https://vsn-pipelines.readthedocs.io/en/latest/features.html#cell-based-metadata-filtering
 
@@ -752,7 +752,7 @@ In the generated .config file, make sure the ``file_paths`` parameter is set wit
 
 - The ``suffix`` parameter is used to infer the sample name from the file paths (it is removed from the input file path to derive a sample name).
 
-In case there are multiple .h5ad files that need to be processed with different suffixes, the multi-labelled strategy should be used to define the h5ad param::
+In case there are multiple .h5ad files that need to be processed with different suffixes, the multi-labelled strategy should be used to define the h5ad parameter::
 
     [...]
     data {