fix by running prettier

README.md

@@ -38,16 +38,16 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 13. To Call SNVs either path a or b can be followed. Path A will run by default
     a. Call SNVs
     1. ([`BCFtools Mpileups`](https://samtools.github.io/bcftools/bcftools.html#mpileup))
-15. b. Call SNVs
+14. b. Call SNVs
     1. Split cigar reads ([`SplitN Cigar Reads`](https://gatk.broadinstitute.org/hc/en-us/articles/360036858811-SplitNCigarReads))
     2. Haplotype caller ([`Haplotype Caller`](https://gatk.broadinstitute.org/hc/en-us/articles/360037225632-HaplotypeCaller))
     3. Variant filtration ([`Variant Filtration`](https://gatk.broadinstitute.org/hc/en-us/articles/360037434691-VariantFiltration))
     4. BCFtools statistics ([`BCFtools stats`](https://samtools.github.io/bcftools/bcftools.html#stats))
-16. Allele Specific Read Counter ([`ASEReadCounter`](https://gatk.broadinstitute.org/hc/en-us/articles/360037428291-ASEReadCounter))
-17. Assess allelic imbalance ([`BootstrapAnn`](https://github.com/J35P312/BootstrapAnn#bootstrapann))
-18. Annotation ([`VEP`](https://github.com/Ensembl/ensembl-vep))
-19. Alignment QC ([`Picard CollectRnaSeqMetrics`](https://broadinstitute.github.io/picard/))
-20. Present QCs ([`MultiQC`](http://multiqc.info/))
+15. Allele Specific Read Counter ([`ASEReadCounter`](https://gatk.broadinstitute.org/hc/en-us/articles/360037428291-ASEReadCounter))
+16. Assess allelic imbalance ([`BootstrapAnn`](https://github.com/J35P312/BootstrapAnn#bootstrapann))
+17. Annotation ([`VEP`](https://github.com/Ensembl/ensembl-vep))
+18. Alignment QC ([`Picard CollectRnaSeqMetrics`](https://broadinstitute.github.io/picard/))
+19. Present QCs ([`MultiQC`](http://multiqc.info/))
 
 ## Usage
 

docs/usage.md

@@ -40,7 +40,7 @@ Table of contents:
 
 ## Introduction
 
-**tomte** is a bioinformatics best-practice analysis pipeline for analysing  RNAseq data from patients with rare diseases.
+**tomte** is a bioinformatics best-practice analysis pipeline for analysing RNAseq data from patients with rare diseases.
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!