Merge pull request #92 from bioinformaticsguy/docs-fixes

docs: Documentation only changes

README.md

@@ -45,19 +45,19 @@ Activate the conda environment:
 
 Test your configuration by performing a dry-run via
 
-    snakemake --use-conda --configfile conf/config.yaml -n
+    snakemake --use-conda --configfile config/config.yaml -n
 
 Execute the workflow locally via
 
-    snakemake --use-conda --cores $N --configfile conf/config.yaml
+    snakemake --use-conda --cores $N --configfile config/config.yaml
 
 using `$N` cores or run it in a cluster environment (SLURM using sbatch) via
 
-    snakemake --use-conda --configfile conf/config.yaml --cluster "sbatch --nodes=1 --ntasks={cluster.threads} --mem={cluster.mem} -t {cluster.time} -p {cluster.queue} -o {cluster.output}" --jobs 100 --cluster-config config/sbatch.yaml
+    snakemake --use-conda --configfile config/config.yaml --cluster "sbatch --nodes=1 --ntasks={cluster.threads} --mem={cluster.mem} -t {cluster.time} -p {cluster.queue} -o {cluster.output}" --jobs 100 --cluster-config config/sbatch.yaml
 
 or
 
-    snakemake --use-conda --configfile conf/config.yaml --drmaa "-n {cluster.threads} --mem={cluster.mem} -t {cluster.time} -p {cluster.queue} -o {cluster.output}" --jobs 100
+    snakemake --use-conda --configfile config/config.yaml --drmaa "-n {cluster.threads} --mem={cluster.mem} -t {cluster.time} -p {cluster.queue} -o {cluster.output}" --jobs 100
 
 using DRMAA.
 
@@ -69,7 +69,7 @@ For other cluster environments please check the [Snakemake](https://snakemake.re
 
 If you not only want to fix the software stack but also the underlying OS, use
 
-    snakemake --use-conda --use-singularity --configfile conf/config.yaml
+    snakemake --use-conda --use-singularity --configfile config/config.yaml
 
 in combination with any of the modes above.
 
@@ -83,7 +83,7 @@ See the [Snakemake documentation](https://snakemake.readthedocs.io/en/stable/exe
 
 After successful execution, you can create a self-contained interactive HTML report with all results via:
 
-    snakemake --report report.html --configfile conf/config.yaml
+    snakemake --report report.html --configfile config/config.yaml
 
 This report can, e.g., be forwarded to your collaborators.
 

docs/config.rst

@@ -4,14 +4,14 @@
 Config File
 =====================
 
-The config file is a yaml file that contains the configuration. Different runs can be configured. We recommend to use one config file per MPRA experiment or MPRA roject. But in theory many different experiments can be configured in only one file. It is divided into :code:`global` (generell settings), :code:`assignments` (assigment workflow), and :code:`experiments` (count workflow including variants). This is a full example file with all possible configurations. :download:`config/example_config.yaml <../config/example_config.yaml>`.
+The config file is a yaml file that contains the configuration. Different runs can be configured. We recommend to use one config file per MPRA experiment or MPRA project. But in theory many different experiments can be configured in only one file. It is divided into :code:`global` (generell settings), :code:`assignments` (assigment workflow), and :code:`experiments` (count workflow including variants). This is a full example file with all possible configurations. :download:`config/example_config.yaml <../config/example_config.yaml>`.
 
 .. literalinclude:: ../config/example_config.yaml
    :language: yaml
    :linenos:
 
 
-Note that teh config file is conrolled by jscon schema. This means that the config file is validated against the schema. If the config file is not valid, the program will exit with an error message. The schema is located in :download:`workflow/schemas/config.schema.yaml <../workflow/schemas/config.schema.yaml>`.
+Note that the config file is conrolled by jscon schema. This means that the config file is validated against the schema. If the config file is not valid, the program will exit with an error message. The schema is located in :download:`workflow/schemas/config.schema.yaml <../workflow/schemas/config.schema.yaml>`.
 
 ----------------
 General settings