Merge branch 'dev' into fix-module-warning

README.md

@@ -26,14 +26,14 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 ## Pipeline summary
 
-1. Merge paired-end reads (([`Pear`](https://cme.h-its.org/exelixis/web/software/pear/doc.html)))
+1. Merge paired-end reads ([`Pear`](https://cme.h-its.org/exelixis/web/software/pear/doc.html))
 2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
 3. Adapter trimming ([`Cutadapt`](http://dx.doi.org/10.14806/ej.17.1.200))
 4. Quality filtering ([`Seqtk`](https://github.com/lh3/seqtk))
 5. Read mapping:
-   a. ([`minimap2`](https://github.com/lh3/minimap2), _default_)
-   b. ([`bwa`](http://bio-bwa.sourceforge.net/))
-   c. ([`bowtie2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml))
+   - ([`minimap2`](https://github.com/lh3/minimap2), _default_)
+   - ([`bwa`](http://bio-bwa.sourceforge.net/))
+   - ([`bowtie2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml))
 6. CIGAR parsing for edit calling ([`R`](https://www.r-project.org/))
 
 ## Quick Start