Merge pull request #335 from NBISweden/snakemake-update

Snakemake update

Author: fasterius

pages/jupyter.qmd

@@ -1079,7 +1079,7 @@ interface.
 
 As you can see this notebook contains some brief descriptions in Markdown and
 code to generate a few plots and tables. It uses the output from the MRSA
-case-study Snakemake workflow you worked on in the Snakemake tutorial. This is a
+case-study Snakemake workflow used in the Snakemake tutorial. This is a
 common use-case for Jupyter notebooks; to generate summary statistics and plots
 from the results of a workflow run. (A real-world example could of course
 include a lot more in-depth exploratory analyses).

pages/snakemake.qmd

@@ -1773,7 +1773,7 @@ to be `["results/bowtie2/{genome_id}.1.bt2",
 "results/bowtie2/{genome_id}.2.bt2", ...]`, _i.e._ only expanding the `substr`
 wildcard in the Bowtie2 index. To prevent Snakemake from trying to expand the
 `genome_id` wildcard we have to "mask" it with double curly brackets:
-`{{genome_id}}`.
+`{{{genome_id}}}`.
 
 In addition, we need to replace the hard-coded `results/bowtie2/NCTC8325` in the
 shell directive of the rule with the genome id wildcard. Inside the shell