Merge pull request #636 from drpatelh/updates

Fix HTML tags in output docs
nf-core · May 12, 2021 · 5964998 · 5964998
2 parents 8786f59 + 96e31fa
commit 5964998
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Showing 3 changed files with 3 additions and 12 deletions.
diff --git a/.editorconfig b/.editorconfig
@@ -11,10 +11,6 @@ indent_style = space
 [*.{yml,yaml}]
 indent_size = 2
 
-# These files are linted by markdownlint anyway
-[*.{md,MD,markdown}]
-indent_size = unset
-
 # These files are edited and tested upstream in nf-core/modules
 [/modules/nf-core/**]
 charset = unset

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[3.1](https://github.com/nf-core/rnaseq/releases/tag/3.1)] - 2021-05-12
+## [[3.1](https://github.com/nf-core/rnaseq/releases/tag/3.1)] - 2021-05-13
 
 ### :warning: Major enhancements
 
@@ -15,7 +15,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
-* Fix SALMON_SE_TRANSCRIPT process. It was removing the first sample in the matrix
 * Updated pipeline template to nf-core/tools `1.14`
 * Only FastQ files that require to be concatenated will be passed to `CAT_FASTQ` process
 * [[#449](https://github.com/nf-core/modules/pull/449)] - `--genomeSAindexNbases` will now be auto-calculated before building STAR indices

diff --git a/docs/output.md b/docs/output.md
@@ -601,15 +601,11 @@ We also explore higher components in terms of experimental factors inferred from
 
 The plot on the left hand side shows the standard PC plot - notice the variable number of underscores, meaning that the central plot would not be produced: here we have changed the underscore that is hyphenating the treatment to a '-' character. This allows the central plot to be generated, and we can see that replicate (the 2nd part of the sample name) seems to be affecting the 3rd principal component, but the treatment factor is affecting the more important first two components. The right-most plot shows all pairwise euclidean distances between the samples.
 
-<p markdown="1" align="center">
-  <img src="images/deseq2_qc_plots.png" alt="DESeq2 PCA plots">
-</p>
+<p align="center"><img src="images/deseq2_qc_plots.png" alt="DESeq2 PCA plots"></p>
 
 ![MultiQC - DESeq2 PCA plot](images/mqc_deseq2_pca.png)
 
-<p markdown="1" align="center">
-  <img src="images/mqc_deseq2_clustering.png" alt="MultiQC - DESeq2 sample similarity plot" width="600">
-</p>
+<p align="center"><img src="images/mqc_deseq2_clustering.png" alt="MultiQC - DESeq2 sample similarity plot" width="600"></p>
 
 ### MultiQC