Set cores

_episodes/02-snakefiles.md

@@ -81,11 +81,15 @@ By default, Snakemake looks for a file called `Snakefile`, and we can run
 Snakemake as follows:
 
 ~~~
-snakemake
+snakemake --cores 1
 ~~~
 {: .language-bash}
 
-By default, Snakemake tells us what it's doing as it executes actions:
+The number of cores to use is a required argument for versions 5.11 and 
+above of Snakemake.  It is possible to use more cores, but a single core 
+is sufficient for now.  It is also possible to indicate the number of
+cores using `-c`, which will be used going forward. By default, 
+Snakemake tells us what it's doing as it executes actions:
 
 ~~~
 Provided cores: 1
@@ -123,7 +127,7 @@ The first 5 lines of `isles.dat` should look exactly like before.
 > using the `-s` flag. For example, if our Snakefile is named `MyOtherSnakefile`:
 >
 > ~~~
-> snakemake -s MyOtherMakefile
+> snakemake -c 1 -s MyOtherSnakefile
 > ~~~
 >{: .language-bash}
 >
@@ -166,7 +170,7 @@ its dependency:
 If we run Snakemake again,
 
 ~~~
-snakemake
+snakemake -c 1
 ~~~
 {: .language-bash}
 
@@ -225,7 +229,7 @@ rule count_words_abyss:
 If we run Snakemake,
 
 ~~~
-snakemake
+snakemake -c 1
 ~~~
 {: .language-bash}
 
@@ -242,7 +246,7 @@ and this rule is already up-to-date. We need to explicitly tell Snakemake we
 want to build `abyss.dat`:
 
 ~~~
-snakemake abyss.dat
+snakemake -c 1 abyss.dat
 ~~~
 {: .language-bash}
 
@@ -279,7 +283,7 @@ Finished job 0.
 > If we ask Snakemake to build a file which does not have a
 > rule in our Snakefile, then we get messages like:
 > ~~~
-> $ snakemake what.dat
+> $ snakemake -c 1 what.dat
 > MissingRuleException:
 > No rule to produce what.dat (if you use input functions make sure that they
 > don't raise unexpected exceptions).
@@ -308,7 +312,7 @@ remove the data files whether or not they exist. If we run Snakemake and specify
 this target:
 
 ~~~
-snakemake clean
+snakemake -c 1 clean
 ~~~
 {: .language-bash}
 
@@ -369,7 +373,7 @@ to trigger the build of its dependencies, if needed.
 If we run,
 
 ~~~
-snakemake dats
+snakemake -c 1 dats
 ~~~
 {: .language-bash}
 
@@ -415,7 +419,7 @@ If we run `dats` again, then snakemake will see that the dependencies
 no actions, there is `nothing to be done`:
 
 ~~~
-snakemake dats
+snakemake -c 1 dats
 ~~~
 {: .language-bash}
 
@@ -461,8 +465,8 @@ prints out commands instead of actually executing them. Very useful for
 debugging!
 
 ~~~
-snakemake clean
-snakemake -n -p isles.dat
+snakemake -c 1 clean
+snakemake -c 1 -n -p isles.dat
 ~~~
 {: .language-bash}
 

_episodes/03-wildcards.md

@@ -119,7 +119,7 @@ Let's update our text files and re-run our rule:
 
 ~~~
 touch books/*.txt
-snakemake results.txt
+snakemake -c 1 results.txt
 ~~~
 {: .language-bash}
 
@@ -176,7 +176,7 @@ Finished job 0.
 >
 > ~~~
 > touch *.dat
-> snakemake results.txt
+> snakemake -c 1 results.txt
 > ~~~
 > {: .language-bash}
 >
@@ -196,7 +196,7 @@ Finished job 0.
 > >
 > > ~~~
 > > touch books/*.txt
-> > snakemake results.txt
+> > snakemake -c 1 results.txt
 > > ~~~
 > >{: .language-bash}
 > >
@@ -267,7 +267,7 @@ Let's mark `wordcount.py` as updated, and re-run the pipeline:
 
 ~~~
 touch wordcount.py
-snakemake
+snakemake -c 1
 ~~~
 {: .language-bash}
 
@@ -317,7 +317,7 @@ files. However, it turns out we don't have to! Let's see what happens to
 
 ~~~
 touch wordcount.py
-snakemake results.txt
+snakemake -c 1 results.txt
 ~~~
 {: .language-bash}
 
@@ -374,7 +374,7 @@ steps.
 >
 > ~~~
 > touch books/last.txt
-> snakemake results.txt
+> snakemake -c 1 results.txt
 > ~~~
 > {: .language-bash}
 >

_episodes/04-patterns.md

@@ -48,8 +48,8 @@ Let's test the new pattern rule. We use the -p option to show that it is
 running things correctly:
 
 ~~~
-snakemake clean
-snakemake -p dats
+snakemake -c 1 clean
+snakemake -c 1 -p dats
 ~~~
 {: .language-bash}
 
@@ -58,7 +58,7 @@ to build individual `.dat` targets as before, and that our new rule will work
 no matter what stem is being matched.
 
 ~~~
-snakemake -p sierra.dat
+snakemake -c 1 -p sierra.dat
 ~~~
 {: .language-bash}
 
@@ -98,7 +98,7 @@ Finished job 0.
 > such as `snakemake clean`, you cannot execute a pattern rule this way:
 >
 > ~~~
-> snakemake count_words
+> snakemake -c 1 count_words
 > ~~~
 > {:.language-bash}
 > ~~~

_episodes/05-snakemake-python.md

@@ -45,7 +45,7 @@ rule zipf_test:
 ~~~
 {: .language-python}
 
-After updating your rule, run `snakemake clean` and `snakemake -p` to confirm
+After updating your rule, run `snakemake -c 1 clean` and `snakemake -c 1 -p` to confirm
 that the pipeline still works.
 
 > ## Named Dependencies
@@ -94,7 +94,7 @@ one place to update the list of files to process.
 > Update your Snakefile with the `DATS` global variable.
 >
 > Try recreating both the `dats` and `results.txt` targets
-> (run `snakemake clean` in between).
+> (run `snakemake -c 1 clean` in between).
 >
 > > ## Solution
 > >
@@ -121,10 +121,10 @@ rule zipf_test:
 ~~~
 {: .language-python}
 
-Now let's clean up our workspace with `snakemake clean`:
+Now let's clean up our workspace with `snakemake -c 1 clean`:
 
 ~~~
-snakemake clean
+snakemake -c 1 clean
 ~~~
 {: .language-bash}
 
@@ -148,7 +148,7 @@ Finished job 0.
 Now let's re-run the pipeline...
 
 ~~~
-snakemake
+snakemake -c 1
 ~~~
 {: .language-bash}
 
@@ -202,7 +202,7 @@ Finished job 0.
 Let's do a dry-run:
 
 ~~~
-snakemake -n
+snakemake -c 1 -n
 ~~~
 {: .language-bash}
 
@@ -392,7 +392,7 @@ Upon execution of the corresponding rule, Snakemake runs our Python code
 in the `run:` block:
 
 ~~~
-snakemake --quiet print_book_names
+snakemake -c 1 print_book_names --quiet rules
 ~~~
 {: .language-bash}
 
@@ -417,10 +417,11 @@ Finished job 0.
 ~~~
 {: .output}
 
-> ## Note the `--quiet` option
+> ## Note the `--quiet rules` option
 >
-> `--quiet` or `-q` suppresses a lot of the rule progress output from Snakemake.
-> This can be useful when you just want to see your own output.
+> `--quiet rules` or `-q rules` suppresses a lot of the rule progress output from Snakemake.
+> This can be useful when you just want to see your own output. Other choices are
+> `-q all` and `-q progress`.
 {:.callout}
 
 [ref-dependency]: ../reference#dependency

_episodes/06-remaining-stages.md

@@ -114,14 +114,14 @@ directory.
 > build a specific file with a command like:
 >
 > ~~~
-> snakemake last.dat
+> snakemake -c 1 last.dat
 > ~~~
 > {:.language-bash}
 >
 > After moving the location of `dat` files, the correct command is:
 >
 > ~~~
-> snakemake dats/last.dat
+> snakemake -c 1 dats/last.dat
 > ~~~
 > {:.language-bash}
 >
@@ -174,7 +174,7 @@ directory.
 ## Default Rules
 
 The default rule is the rule that Snakemake runs if you don't specify a rule
-on the command-line (e.g.: if you just run `snakemake`).
+on the command-line (e.g.: if you just run `snakemake -c 1`).
 
 The default rule is simply the first rule in a Snakefile. While the default
 rule can be anything you like, it is common practice to call the default rule
@@ -228,8 +228,8 @@ It is common practice to have a `clean` rule that deletes all intermediate
 and generated files, taking your workflow back to a blank slate.
 
 We already have a `clean` rule, so now is a good time to check that it
-removes all intermediate and output files. First do a `snakemake all` followed
-by `snakemake clean`. Then check to see if any output files remain and add them
+removes all intermediate and output files. First do a `snakemake -c 1 all` followed
+by `snakemake -c 1 clean`. Then check to see if any output files remain and add them
 to the clean rule if required.
 
 ## Creating an Archive
@@ -252,7 +252,7 @@ In this case, we will create an archive tar file.
 > * The archive should contain all `dat` files, plots, and the
 > Zipf summary table (`results.txt`).
 > * Update `all` to expect `zipf_analysis.tar.gz` as input.
-> * Remove the archive when `snakemake clean` is called.
+> * Remove the archive when `snakemake -c 1 clean` is called.
 >
 > The syntax to create an archive is:
 > ~~~