diff --git a/.github/markdownlint.yml b/.github/markdownlint.yml index 96b12a703..b9f0f5a24 100644 --- a/.github/markdownlint.yml +++ b/.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 diff --git a/CHANGELOG.md b/CHANGELOG.md index e648a7a23..d30eb42e0 100644 --- a/CHANGELOG.md +++ b/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` diff --git a/README.md b/README.md index 35ba91149..bb352be58 100644 --- a/README.md +++ b/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.**. diff --git a/docs/images/eager_icon.svg b/docs/images/eager_icon.svg new file mode 100644 index 000000000..c3df7a3ed --- /dev/null +++ b/docs/images/eager_icon.svg @@ -0,0 +1,204 @@ + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/images/nf-core_eager_logo.png b/docs/images/nf-core_eager_logo.png new file mode 100644 index 000000000..959bd752a Binary files /dev/null and b/docs/images/nf-core_eager_logo.png differ diff --git a/docs/images/nf-core_eager_logo.svg b/docs/images/nf-core_eager_logo.svg new file mode 100644 index 000000000..b62957265 --- /dev/null +++ b/docs/images/nf-core_eager_logo.svg @@ -0,0 +1,283 @@ + + + +image/svg+xmlnf- +core/ +eager + \ No newline at end of file diff --git a/docs/output.md b/docs/output.md index 767d3a4ee..db7563ef0 100644 --- a/docs/output.md +++ b/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.

- +

#### Sequence Quality Histograms @@ -122,7 +122,6 @@ You will often see that the first 5 or so bases have slightly lower quality than

- Things to watch out for: * all positions having Phred scores less than 27