Merge pull request #11 from nf-core/dev

Syncing

.github/markdownlint.yml

@@ -3,3 +3,7 @@ default: true,
 line-length: false
 no-duplicate-header:
     siblings_only: true
+no-inline-html: 
+    allowed_elements:
+        - img
+        - p

CHANGELOG.md

@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * [#212](https://github.com/nf-core/eager/issues/212) - Added ability to use only mergedreads downstream from Adapterremoval
 * [#265](https://github.com/nf-core/eager/issues/265) - Adjusted full markdown linting in Travis CI
 * [#247](https://github.com/nf-core/eager/issues/247) - Added nuclear contamination with angsd
+* Fancy new logo from [ZandraFagernas](https://github.com/ZandraFagernas)
 
 ### `Fixed`
 

README.md

@@ -1,4 +1,4 @@
-# ![nf-core/eager](docs/images/eager_logo.png)
+# ![nf-core/eager](docs/images/nf-core_eager_logo.png)
 
 **A fully reproducible ancient and modern DNA pipeline in Nextflow and with cloud support.**.
 

docs/output.md

@@ -109,7 +109,7 @@ This shows a barplot with the overall number of sequences (x axis) in your raw l
 A section of the bar will also show an approximate estimation of the fraction of the total number of reads that are duplicates of another. This can derive from over-amplifcation of the library, or lots of single adapters. This can be later checked with the Deduplication check. A good library and sequencing run should have very low amounts of duplicates reads.
 
 <p align="center">
-	<img src="images/output/fastqc/sequence_counts.png" width="75%" height = "75%">
+  <img src="images/output/fastqc/sequence_counts.png" width="75%" height = "75%">
 </p>
 
 #### Sequence Quality Histograms
@@ -122,7 +122,6 @@ You will often see that the first 5 or so bases have slightly lower quality than
   <img src="images/output/fastqc/sequencing_quality_histogram.png" width="75%" height = "75%">
 </p>
 
-
 Things to watch out for:
 
 * all positions having Phred scores less than 27