Long URLs should maybe be ref-links?

carpentries-incubator · Jan 10, 2024 · b725003 · b725003
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diff --git a/_extras/discuss.md b/_extras/discuss.md
@@ -89,8 +89,7 @@ individual to individual!
 
 > ## Running Many Serial BLAST+ Analyses in Parallel
 >
-> [BLAST+](
-https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
+> [BLAST+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
 > finds regions of similarity between biological sequences. The program
 > compares nucleotide or protein sequences to sequence databases and calculates
 > the statistical significance.
@@ -107,14 +106,12 @@ https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Do
 >
 > We have prepared an example dataset that has 100 sequences to analyse
 > (actually this is 10 sequences repeated 10 times). This set is based on the
-> [BLAST GNU Parallel example](
-https://github.com/LangilleLab/microbiome_helper/wiki/Quick-Introduction-to-GNU-Parallel)
+> [BLAST GNU Parallel example](https://github.com/LangilleLab/microbiome_helper/wiki/Quick-Introduction-to-GNU-Parallel)
 >
 > This exercise involves:
 >
 > - Downloading and expanding the dataset to the HPC system from:
->   [{{ site.url }}{{site.baseurl }}/files/parallel_example.tar.gz](
->   {{ site.url }}{{site.baseurl }}/files/parallel_example.tar.gz)
+>   [{{ site.url }}{{site.baseurl }}/files/parallel_example.tar.gz]({{ site.url }}{{site.baseurl}}/files/parallel_example.tar.gz)
 > - Writing a job submission script to run a single analysis using the `blast`
 >   module and the following command:
 >

diff --git a/_extras/guide.md b/_extras/guide.md
@@ -66,8 +66,7 @@ is a great way to contribute.
 :    *to be defined*
 
 [Supercomputer](https://en.wikipedia.org/wiki/Supercomputer)
-:    ["... a major scientific instrument ..."](
-https://www.hpcnotes.com/2015/10/essential-analogies-for-hpc-advocate.html)
+:    ["... a major scientific instrument ..."](https://www.hpcnotes.com/2015/10/essential-analogies-for-hpc-advocate.html)
 
 [Workstation](https://en.wikipedia.org/wiki/Workstation)
 :    *to be defined*

diff --git a/_extras/learner-prerequisites.md b/_extras/learner-prerequisites.md
@@ -14,8 +14,7 @@ bring all prerequisites to the course.
 ## Pre-Workshop Survey
 
 For a motivation of this survey type, see Greg Wilson's template in [Teaching
-Tech Together](
-https://teachtogether.tech/en/index.html#s:checklists-preassess).
+Tech Together](https://teachtogether.tech/en/index.html#s:checklists-preassess).
 
 ### Shell