spell check workflows

docs/tutorial/advanced_workflow.md

@@ -28,5 +28,5 @@ The workflows are available in:
 - *mark05* : assessing the MCMC tree dispersion per tree-tree metric as
   a baseline to understand the tree-tree metric.
 
-The outcome an analyis of the results is available in the
+The outcome and analysis of the results are available in the
 [thesis](TODO:%20(gordonkoehn)%20add%20thesis%20here.).

docs/tutorial/advanced_workflow.qmd

@@ -24,4 +24,4 @@ The workflows are available in:
 
 * _mark05_ :  assessing the MCMC tree dispersion per tree-tree metric as a baseline to understand the tree-tree metric.
 
-The outcome an analyis of the results is available in the [thesis](TODO: (gordonkoehn) add thesis here.).
+The outcome and analysis of the results are available in the [thesis](TODO: (gordonkoehn) add thesis here.).

docs/tutorial/basicWorkflows.md

@@ -1,60 +1,59 @@
 # Basic Workflows
 
-*PYggdrasil* implements a number of basic workflows for simulated
-mutation profile experiments.
+*PYggdrasil* implements several basic workflows for simulated mutation
+profile experiments.
 
 We originally used these workflows as part of larger experiments to
-evaluate SCITEs performance.
+evaluate SCITE’s performance.
 
-Here we show the workflow to run a SCITE mutation profile simulation and
-inference experiment. We visualize the evolution of the chains via the
-log probability and two similarity measures.
+Here, we show the workflow to run a SCITE mutation profile simulation
+and inference experiment. We visualize the evolution of the chains via
+the log probability and two similarity measures.
 
-In `workflows/` we define a number of
+In `workflows/`, we define several
 [Snakemake](https://snakemake.readthedocs.io/en/stable/) workflows.
-These workflows are defined in a modular way, so that they can be easily
+These workflows are defined in a modular way so that they can be easily
 combined to create more complex workflows.
 
-- `workflows/tree_inference.smk` is the main workflow, which runs a
-  mutation profile simulation and inference experiment.
-- `workflows/anayze.smk` is a workflow to analyze the results of a
-  simulation and inference experiment.
-- `workflows/visualize.smk` is a workflow to visualize the results of a
+- `workflows/tree_inference.smk` implements rules which run a mutation
+  profile simulation and inference experiment.
+- `workflows/anayze.smk` implements rules to analyze the results of a
   simulation and inference experiment.
+- `workflows/visualize.smk` implements rules to visualize the results of
+  a simulation and inference experiment.
 
-All the `markXX` rules are used to to define more complex workflows
-using these basic functionality. These experiments are defined in
-`workflows/markXX.smk` and are part of
-[gordonkoehn](https://github.com/gordonkoehn) thesis.
+All the `markXX` rules define more complex workflows using these basic
+functionalities. These experiments are defined in `workflows/markXX.smk`
+and are part of [gordonkoehn](https://github.com/gordonkoehn)’s thesis.
 
-Here we show how the basic workflows can work together to run a single
-MCMC chain and visualize the results. All steps of a workflow are
-designed to yield intermediate results saved to the disk. Each file is
-named in a unique way, so that it can be easily identified and used in
-other workflows. A filename implies the complete history of generation!
-(This results in long fielnames, but allows us to use pure string
-mattching in snakemake – like magic.)
+Here, we show how the basic workflows can work together to run a single
+MCMC chain and visualize the results. All workflow steps are designed to
+yield intermediate results saved to the disk. Each file is named
+uniquely to be easily identified and used in other workflows. A filename
+implies the complete history of its generation! (This results in long
+filenames but allows us to use pure string matching in snakemake – like
+magic.)
 
 ## Run a single MCMC chain
 
 Here is how you would run the *mark04* workflow.
 
 ``` {zsh}
- # navigate to the workflows directory
+ # navigate to the workflow directory
  cd workflows
- # run the mark00 workflow  with 4 cores
+ # run the mark00 workflow  with four cores
  snakemake -c 4 mark00
 ```
 
-Note before you can run it, you need to install *snakemake* at best in a
-conda environment. See
+Note: before you can run it, you need to install *snakemake* at best in
+a conda environment. See
 [workflows/README.md](https://github.com/cbg-ethz/PYggdrasil/blob/main/workflows/README.md)
 for more details.
 
 *Also, you need to adjust the paths of the *DATADIR* and *REPODIR* in
-*workflows/mark00.smk* and *workflows/tree_inference.smk*!*
+`workflows/mark00.smk_` and `workflows/tree_inference.smk`!*
 
-Once you get it running: Here is what is happening the below diagram
+Once you get it running, Here is what is happening; the diagram below
 shows the DAG of the *mark00* workflow.
 
 ![mark00 directed acyclic graph of
@@ -70,24 +69,24 @@ The core rules here are
 
 - gen_cell_simulation to generate a simulated mutation profile given a
   tree,
-
-- *mcmcm* running the inference and
-
+- *mcmc* running the inference and
 - *analyze_metrics* to compute the similarity metrics.
 
-For the rest of the rules see the the individual files: \*
-`workflows/tree_inference.smk` \* `workflows/anayze.smk` \*
-`workflows/visualize.smk`
+For the rest of the rules, see the individual files:
+
+- `workflows/tree_inference.smk`
+- `workflows/analyze.smk`
+- `workflows/visualize.smk`
 
-The full workflow generated a these three files:
+The full workflow generated these three files:
 
 ![mark00 log-prob evolution](basicWorkflows_files/log_prob.svg)
 
 ![mark00 MP3 evolution](basicWorkflows_files/MP3.svg)
 
-Note the AD is a bad matric to visualize here, as we use a star tree as
+Note the AD is a bad metric to visualize here, as we use a star tree as
 a ground truth. No matter what the inference does, the AD will always be
-0, as no ancestor-descendant relationship is present per definition of a
-star tree.
+0, as no ancestor-descendant relationship is present per the definition
+of a star tree.
 
 ![mark00 AD evolution](basicWorkflows_files/AD.svg)

docs/tutorial/basicWorkflows.qmd

@@ -4,45 +4,45 @@ format: gfm
 jupyter: python3
 ---
 
-_PYggdrasil_ implements a number of basic workflows for simulated mutation profile experiments.
+_PYggdrasil_ implements several basic workflows for simulated mutation profile experiments.
 
-We originally used these workflows as part of larger experiments to evaluate SCITEs performance. 
+We originally used these workflows as part of larger experiments to evaluate SCITE's performance. 
 
-Here we show the workflow to run a SCITE mutation profile simulation and inference experiment.
+Here, we show the workflow to run a SCITE mutation profile simulation and inference experiment.
 We visualize the evolution of the chains via the log probability and two similarity measures.
 
-In `workflows/` we define a number of [Snakemake](https://snakemake.readthedocs.io/en/stable/) workflows.
-These workflows are defined in a modular way, so that they can be easily combined to create more complex workflows.
+In `workflows/`, we define several [Snakemake](https://snakemake.readthedocs.io/en/stable/) workflows.
+These workflows are defined in a modular way so that they can be easily combined to create more complex workflows.
 
-* `workflows/tree_inference.smk` is the main workflow, which runs a mutation profile simulation and inference experiment.
-* `workflows/anayze.smk` is a workflow to analyze the results of a simulation and inference experiment.
-* `workflows/visualize.smk` is a workflow to visualize the results of a simulation and inference experiment.
+* `workflows/tree_inference.smk` implements rules which run a mutation profile simulation and inference experiment.
+* `workflows/anayze.smk` implements rules to analyze the results of a simulation and inference experiment.
+* `workflows/visualize.smk` implements rules to visualize the results of a simulation and inference experiment.
 
-All the `markXX` rules are used to to define more complex workflows using these basic functionality.
-These experiments are defined in `workflows/markXX.smk` and are part of [gordonkoehn](https://github.com/gordonkoehn) thesis.
+All the `markXX` rules define more complex workflows using these basic functionalities.
+These experiments are defined in `workflows/markXX.smk` and are part of [gordonkoehn](https://github.com/gordonkoehn)'s thesis.
 
-Here we show how the basic workflows can work together to run a single MCMC chain and visualize the results.
-All steps of a workflow are designed to yield intermediate results saved to the disk. 
-Each file is named in a unique way, so that it can be easily identified and used in other workflows.
-A filename implies the complete history of generation! 
-(This results in long fielnames, but allows us to use pure string mattching in snakemake -- like magic.)
+Here, we show how the basic workflows can work together to run a single MCMC chain and visualize the results.
+All workflow steps are designed to yield intermediate results saved to the disk. 
+Each file is named uniquely to be easily identified and used in other workflows.
+A filename implies the complete history of its generation! 
+(This results in long filenames but allows us to use pure string matching in snakemake -- like magic.)
 
 ## Run a single MCMC chain
 
 Here is how you would run the _mark04_ workflow.
 ```{zsh}
- # navigate to the workflows directory
+ # navigate to the workflow directory
  cd workflows
- # run the mark00 workflow  with 4 cores
+ # run the mark00 workflow  with four cores
  snakemake -c 4 mark00
  ```
 
-Note before you can run it, you need to install _snakemake_ at best in a conda environment.
+Note: before you can run it, you need to install _snakemake_ at best in a conda environment.
 See [workflows/README.md](https://github.com/cbg-ethz/PYggdrasil/blob/main/workflows/README.md) for more details.
 
-*Also, you need to adjust the paths of the _DATADIR_ and _REPODIR_ in _workflows/mark00.smk_ and _workflows/tree_inference.smk_!*
+*Also, you need to adjust the paths of the _DATADIR_ and _REPODIR_ in `workflows/mark00.smk_` and `workflows/tree_inference.smk`!*
 
-Once you get it running: Here is what is happening the below diagram shows the DAG of the _mark00_ workflow.
+Once you get it running, Here is what is happening; the diagram below shows the DAG of the _mark00_ workflow.
 
 ![mark00 directed acyclic graph of workflow](basicWorkflows_files/dag_mark00.png)
 
@@ -55,23 +55,23 @@ This graphic was generated by the following command:
 The core rules here are 
 
 * gen_cell_simulation to generate a simulated mutation profile given a tree,
-* _mcmcm_ running the inference and 
+* _mcmc_ running the inference and 
 * _analyze_metrics_ to compute the similarity metrics.
 
-For the rest of the rules see the the individual files:
+For the rest of the rules, see the individual files:
 
 * `workflows/tree_inference.smk` 
-* `workflows/anayze.smk` 
+* `workflows/analyze.smk` 
 * `workflows/visualize.smk` 
 
-The full workflow generated a these three files:
+The full workflow generated these three files:
 
 ![mark00 log-prob evolution](basicWorkflows_files/log_prob.svg)
 
 ![mark00 MP3 evolution](basicWorkflows_files/MP3.svg)
 
-Note the AD is a bad matric to visualize here, as we use a star tree as a ground truth.
-No matter what the inference does, the AD will always be 0, as no ancestor-descendant relationship is present per definition of a star tree.
+Note the AD is a bad metric to visualize here, as we use a star tree as a ground truth.
+No matter what the inference does, the AD will always be 0, as no ancestor-descendant relationship is present per the definition of a star tree.
 
 ![mark00 AD evolution](basicWorkflows_files/AD.svg)