typos

Author: gwct

docs/resources/Tutorials/add-to-whole-genome-alignment-cactus.md

@@ -159,7 +159,7 @@ In order to run the last step of the workflow that converts the HAL format to a
 
 ??? info "The Cactus update input file"
 
-    The various Cactus commands depend on a single input file with information about the genomes to align. This file is automatically generated by the pipeline at `[output_dir]/cactus-update-input.txt`. This file is a simple tab delimited file and should contains line:
+    The various Cactus commands depend on a single input file with information about the genomes to align. This file is automatically generated by the pipeline at `[output_dir]/cactus-update-input.txt`. This file is a simple tab delimited file and should contain one line:
 
     ```
     [tip label to add to tree]   [path/to/genome/fasta.file]    [new branch length to add to the tree]

docs/resources/Tutorials/replace-genome-whole-genome-alignment-cactus.md

@@ -127,7 +127,7 @@ which would result in:
 ((simHuman_chr6:0.144018,(simMouse_chr6:0.084509,simRat_chr6:0.091589)mr:0.271974)Anc1:0.020593,(simCow_chr6:0.18908,simDog_chr6:0.16303)Anc2:0.032898)Anc0;
 ```
 
-If we want to replace the *simHuman_chr6* genome in our HAL with a new version of the sequence, we would set this label in our config file below.
+If we want to replace the *simHuman_chr6* genome in our HAL with a new version of the sequence, we would set this label as the value for `replace:` in our Snakemake config file below.
 
 You can also run `halStats --genomes example.hal` to print out the labels without the Newick tree formatting.
 
@@ -137,13 +137,13 @@ You can also run `halStats --genomes example.hal` to print out the labels withou
 
 ### Reference sample
 
-In order to run the last step of the workflow that converts the HAL format to a readable MAF format (See [pipeline outputs](#pipeline-outputs) for more info), you will need to select one assembly as a reference assembly. The reference assembly's coordinate system will be used for projection to MAF format. You should indicate the reference assembly in the Snakemake config file (outlined below). For instance, if I wanted my reference sample in the above tree to be the genome labeled **1** in the tree, I would put the string `1` in the `maf_reference:` line of the Snakemake config file.
+In order to run the last step of the workflow that converts the HAL format to a readable MAF format (See [pipeline outputs](#pipeline-outputs) for more info), you will need to select one assembly as a reference assembly. The reference assembly's coordinate system will be used for projection to MAF format. You should indicate the reference assembly in the Snakemake config file (outlined below). For instance, if I wanted my reference sample in the above tree to be the genome labeled **simHuman_chr6** in the tree, I would put the string `simHuman_chr6` in the `maf_reference:` line of the Snakemake config file.
 
 ### Preparing the Snakemake config file
 
-??? info "The Cactus update input file"
+??? info "The Cactus replace input file"
 
-    The various Cactus commands depend on a single input file with information about the genomes to align. This file is automatically generated by the pipeline at `[output_dir]/cactus-replace-input.txt`. This file is a simple tab delimited file and should contains line:
+    The various Cactus commands depend on a single input file with information about the genomes to align. This file is automatically generated by the pipeline at `[output_dir]/cactus-replace-input.txt`. This file is a simple tab delimited file and should contain one line:
 
     ```
     [tip label to add to tree]   [path/to/genome/fasta.file]