documentation updates

docs/getting_started/Examples.rst

@@ -36,12 +36,12 @@ Running tRNAnalysis
 
 Command line usage information is available by running::
 
-   trnanalysis trna --help
+   trnanalysis --help
 
 
 The basic syntax for running tRNAnalysis is::
 
-   trnanalysis trna [workflow options] [workflow arguments]
+   trnanalysis [workflow options] [workflow arguments]
 
 
 ``workflow options`` can be one of the following:
@@ -129,7 +129,7 @@ Building tRNAnalysis reports
 
 Reports are generated using the following command once a the `full` command has completed::
 
-    tranalysis trna make build_report
+    tranalysis make build_report
 
 
 .. _getting_started-Troubleshooting:
@@ -154,21 +154,21 @@ resume at the appropriate point.
 .. note::
 
    Look out for upstream errors. For example, you may find that
-   if the pipeline errors and stops, iut may create the file and
+   if the pipeline errors and stops, it may create the file and
    when the pipeline is started again, it will move to the next
    function, despite the previous file being empty. To fix this, delete the files
    created by the last task ran before restarting the pipeline.
 
 Common errors
 -------------
 
-One of the most common errors when runnig the tRNAnalysis is::
+One of the most common errors when running the tRNAnalysis is::
 
     GLOBAL_SESSION = drmaa.Session()
     NameError: name 'drmaa' is not defined
 
-This error occurrs because you are not connected to the cluster. Alternatively
-you can run the pipleine in local mode by adding `- -no-cluster` as a command line option.
+This error occurs because you are not connected to the cluster. Alternatively
+you can run the pipeline in local mode by adding `- -no-cluster` as a command line option.
 
 
 

docs/getting_started/Installation.rst

@@ -12,7 +12,7 @@ The following sections describe how to install tRNAnalysis.
 Conda Installation
 ------------------
 
-The our preferred method of installation is using conda. If you dont have conda installed then
+The our preferred method of installation is using conda. If you don't have conda installed then
 please install conda using `miniconda <https://conda.io/miniconda.html>`_ or `anaconda <https://www.anaconda.com/download/#macos>`_.
 
 We have been experiencing issues with installation because of channel priorities.
@@ -59,10 +59,10 @@ Once checked-out, you can get the latest changes via pulling::
 
 .. _getting_started-Additional:
 
-Installing additonal software
+Installing additional software
 -----------------------------
 
-When building your own workflows we recomend using conda to install software into your environment where possible.
+When building your own workflows we recommend using conda to install software into your environment where possible.
 
 This can easily be performed by::
 

docs/getting_started/Output.rst

@@ -15,9 +15,9 @@ performed.
 The file has the naming convention design_<test>_<control>_<test>_<column>.csv
 
 * `<test>` - refers to the test that you plan to run. There are two options "ltr" or "wald".
-* `<control>` - This is the name of your control condition i.e. the samples you want to test against. This should match on of the samples in the <column> of the file.
-* `<test>` - This is the name of the test condition. This should match with one of the samples in the <column> of the file
-* `<column>` - This is a column that you want to use for your testing in the design_* file
+* `<control>` - This is the name of your control condition i.e. the samples you want to test against. This should match one of the samples within the <column> of the design file.
+* `<test>` - This is the name of the test condition. This should match with one of the samples in the <column> of the design file
+* `<column>` - This is a column name that you want to use for your testing in the design_* file
 
 tRNAnalysis runs DEseq2 under the hood so you can refer to the bioconductor help
 pages for further information on how to set up contrasts for your data.
@@ -51,11 +51,11 @@ Opening the report
 
 Once you have ran the software with the command::
 
-  trnanalysis trna make full
+  trnanalysis make full
 
 and::
 
-  trnanalysis trna make build_report
+  trnanalysis make build_report
 
 a final html report should have been generated.
 

docs/getting_started/Tutorial.rst

@@ -25,7 +25,7 @@ Tutorial start
 **2.** Next we will generate a configuration yml file so the pipeline output can be modified::
 
    cd test_trna
-   trnanalysis trna config
+   trnanalysis config
 
 This will generate a **pipeline.yml** file containing the configuration parameters than can be used to modify
 the output of the pipeline. These parameters can all be modified to change the output or running of tRNAnalysis.
@@ -34,14 +34,14 @@ appropriate in this instance.
 
 .. note::
 
-   There is already a pipeline.yml file within the test data so you dont really need to run the command above this time.
+   There is already a pipeline.yml file within the test data so you don't really need to run the command above this time.
 
 **3.** Next we will run the pipeline::
 
-   trnanalysis trna make full -v5 --no-cluster
+   trnanalysis make full -v5 --no-cluster
 
 This ``--no-cluster`` will run the pipeline locally if you do not have access to a cluster. Alternatively if you have a
-cluster remove the ``--no-cluster`` option and the pipleine will distribute your jobs accross the cluster.
+cluster remove the ``--no-cluster`` option and the pipeline will distribute your jobs across the cluster.
 For information on how to configure your cluster please see the
 `cluster config help <https://trnanalysis.readthedocs.io/en/latest/getting_started/Cluster_config.html>`_.
 
@@ -56,19 +56,19 @@ generated each time the pipeline is ran.
 
 **4.** Generate a report
 
-The final step is to generate a report to display the output of the tRNAnalysis.
+The final step is to generate a report to display the output of tRNAnalysis.
 The tutorial contains all of the files already set up for you to run the report
 without the need to modify any of them. However, we recommend that you look at
 the  :ref:`tRNAnalysis-report` for how to set up the clustering and differential
 expression correctly.
 
 The report is generated by running the command::
 
-    trnanalysis trna make build_report -v 5 --no-cluster
+    trnanalysis make build_report -v 5 --no-cluster
 
 This will generate a MultiQC report in the folder `MultiQC_report.dir/` and an Rmarkdown report in `R_report.dir/Final_report/index.html`.
 
 However, you can access the report by double clicking the FinalReport.html file
-within the directory that tRNAnalysis was executed. 
+within the directory that tRNAnalysis was executed.
 
 This completes the tutorial for running the tRNAnalysis , hope you find it as useful as we do for analysing tRNA sequencing data.