Maybe that gets the tests happy?

.github/workflows/code-test-mac.yml

@@ -46,7 +46,7 @@ jobs:
       run: |
         wget --progress=dot:mega \
           https://github.com/user-attachments/files/16439467/data-for-snakemake-novice-bioinformatics.tar.xz.gz
-        gunzip data-for-snakemake-novice-bioinformatics.tar.xz
+        gunzip data-for-snakemake-novice-bioinformatics.tar.xz.gz
 
         md5sum -c <<<"4522e76f9dddda13e55f7d283638e628  data-for-snakemake-novice-bioinformatics.tar.xz"
 

.github/workflows/code-test-ubuntu.yml

@@ -38,7 +38,7 @@ jobs:
       run: |
         wget --progress=dot:mega \
           https://github.com/user-attachments/files/16439467/data-for-snakemake-novice-bioinformatics.tar.xz.gz
-        gunzip data-for-snakemake-novice-bioinformatics.tar.xz
+        gunzip data-for-snakemake-novice-bioinformatics.tar.xz.gz
 
         md5sum -c <<<"4522e76f9dddda13e55f7d283638e628  data-for-snakemake-novice-bioinformatics.tar.xz"
 

.gitignore

@@ -1,3 +1,5 @@
+/tmp/
+
 # sandpaper files
 episodes/*html
 site/*

.test/ep11.test.sh

@@ -18,8 +18,8 @@ dependencies:
 export SALMON_NO_VERSION_CHECK=1
 snakemake -j1 --sdm conda -p salmon.etoh60_1
 
+conda env list 2>&1
 # A conda env should have been created
-set -x
 conda env list | grep -F /.snakemake/
 
 # But remove it

.test/ep13.test.sh

@@ -1,6 +1,7 @@
 echo "Test for episodes/files/ep13.Snakefile"
 
-cp -vf episodes/files/ep13.Snakefile snakemake_data/yeast/Snakefile
+rm -f snakemake_data/yeast/Snakefile
+cp -v episodes/files/ep13.Snakefile snakemake_data/yeast/Snakefile
 cd snakemake_data/yeast
 
 # This assumes renames are applied
@@ -17,8 +18,9 @@ res2=$( snakemake -Fn -p multiqc | \
 
 # Protected files don't show in the dry-run, so we actually have to make the Kallisto index
 # and then check the perms on it. Then delete it so we don't upset later tests.
+set -x
 rm -f Saccharomyces_cerevisiae.R64-1-1.kallisto_index
-snakemake -j1 -p Saccharomyces_cerevisiae.R64-1-1.kallisto_index
+( umask 0022 ; snakemake -j1 -p Saccharomyces_cerevisiae.R64-1-1.kallisto_index )
 perms=$(stat --format %A Saccharomyces_cerevisiae.R64-1-1.kallisto_index)
 [[ "$perms" == "-r--r--r--" ]]
 rm -vf Saccharomyces_cerevisiae.R64-1-1.kallisto_index

episodes/13-cleaning_up.md

@@ -6,7 +6,7 @@ exercises: 15
 
 ::::::::::::::::::::::::::::::::::::::: objectives
 
-- Understand the function of *temporary* outputs.
+- Understand how Snakemake manages *temporary* outputs
 - Learn about running in *\--touch* mode
 - Learn about *shadow* mode rules
 
@@ -15,7 +15,7 @@ exercises: 15
 :::::::::::::::::::::::::::::::::::::::: questions
 
 - How do I save disk space by removing temporary files?
-- How do I protect important outputs from deletion?
+- How do I isolate the interim files created by jobs from each other?
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
@@ -182,6 +182,9 @@ A related feature is the `protected()` function. This is rather like the opposit
 In practise, Snakemake does this by revoking write permissions on the files
 (as in `chmod -w {output}`).
 
+We can do this for the Salmon and Kallisto indexes, for example, as these should only ever need to
+be generated once.
+
 This works, but can be annoying because Snakemake will refuse to run if it believes it needs to
 re-create a file which is protected. An alternative suggestion is, once you have generated
 an important output file, move or copy the file away from your working directory. That way it will
@@ -279,6 +282,7 @@ this episode.*
 
 - Cleaning up working files is good practise
 - Make use of the `temporary()` function on outputs you don't need to keep
+- Protect outputs which are expensive to reproduce
 - Shadow rules can solve issues with commands that produce unwanted files
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::

episodes/files/ep13.Snakefile

@@ -43,7 +43,7 @@ rule kallisto_quant:
 
 rule kallisto_index:
     output:
-        idx = "{strain}.kallisto_index",
+        idx = protected("{strain}.kallisto_index"),
     input:
         fasta = "transcriptome/{strain}.cdna.all.fa.gz",
     log: "{strain}.kallisto_log"