Pipeline summary report

CHANGELOG.md

@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#558](https://github.com/nf-core/ampliseq/pull/558) - Pipeline summary report
+
 ### `Changed`
 
 ### `Fixed`

README.md

@@ -41,7 +41,8 @@ By default, the pipeline currently performs the following:
 - Excludes unwanted taxa, produces absolute and relative feature/taxa count tables and plots, plots alpha rarefaction curves, computes alpha and beta diversity indices and plots thereof ([QIIME2](https://www.nature.com/articles/s41587-019-0209-9))
 - Calls differentially abundant taxa ([ANCOM](https://www.ncbi.nlm.nih.gov/pubmed/26028277))
 - Creates phyloseq R objects ([Phyloseq](https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html))
-- Overall pipeline run summaries ([MultiQC](https://multiqc.info/))
+- Pipeline QC summaries ([MultiQC](https://multiqc.info/))
+- Pipeline summary report ([R Markdown](https://github.com/rstudio/rmarkdown))
 
 ## Usage
 

assets/nf-core_style.css

@@ -0,0 +1,70 @@
+body {
+  font-family: Calibri, helvetica, sans-serif;
+}
+
+h1 {
+  color: rgb(36, 176, 100);
+  font-size: 200%;
+}
+
+h2 {
+  color: rgb(36, 176, 100);
+  font-size: 150%;
+}
+
+h3 {
+  font-size: 100%;
+  font-weight: bold;
+}
+
+h3.subtitle {
+  font-size: 120%;
+  color: rgb(0, 0, 0);
+  font-weight: bold;
+}
+
+h4 {
+  font-size: 100%;
+  font-weight: bold;
+  font-style: italic;
+}
+
+.watermark {
+  opacity: 0.1;
+  position: fixed;
+  top: 50%;
+  left: 50%;
+  font-size: 500%;
+  color: #24b064;
+}
+
+.list-group-item.active {
+  z-index: 2;
+  color: #fff;
+  background-color: #24b064;
+  border-color: #24b064;
+}
+.list-group-item.active:hover {
+  z-index: 2;
+  color: #fff;
+  background-color: #24b064;
+  border-color: #24b064;
+}
+
+#TOC {
+  background-size: contain;
+  padding-top: 60px !important;
+  background-repeat: no-repeat;
+}
+
+.nav-pills > li.active > a,
+.nav-pills > li.active > a:hover,
+.nav-pills > li.active > a:focus {
+  color: #fff;
+  background-color: #24b064;
+}
+
+a {
+  color: #24b064;
+  text-decoration: none;
+}