[automated] Fix linting with Prettier

fhausmann · Jun 10, 2022 · 82da317 · 82da317
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,21 +14,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Parameters
 
-| Old parameter | New parameter         |
-| ------------- | --------------------- |
-|               | `--mirGeneDB`         |
-|               | `--mirGeneDB_species` |
-|               | `--mirGeneDB_gff`     |
-|               | `--mirGeneDB_mature`  |
-|               | `--mirGeneDB_hairpin` |
-|                      | `--contamination_filter` |
-|                      | `--rrna`                 |
-|                      | `--trna`                 |
-|                      | `--cdna`                 |
-|                      | `--ncrna`                |
-|                      | `--pirna`                |
-|                      | `--other_contamination`  |
-
+| Old parameter | New parameter            |
+| ------------- | ------------------------ |
+|               | `--mirGeneDB`            |
+|               | `--mirGeneDB_species`    |
+|               | `--mirGeneDB_gff`        |
+|               | `--mirGeneDB_mature`     |
+|               | `--mirGeneDB_hairpin`    |
+|               | `--contamination_filter` |
+|               | `--rrna`                 |
+|               | `--trna`                 |
+|               | `--cdna`                 |
+|               | `--ncrna`                |
+|               | `--pirna`                |
+|               | `--other_contamination`  |
 
 ## [v2.0.0](https://github.com/nf-core/smrnaseq/releases/tag/2.0.0) - 2022-05-31 Aqua Zinc Chihuahua
 
@@ -51,11 +50,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Parameters
 
-| Old parameter      | New parameter    |
-| ------------------ | ---------------- |
-| `--conda`            | `--enable_conda`         |
-| `--clusterOptions`   |                          |
-| `--publish_dir_mode` |                          |
+| Old parameter        | New parameter    |
+| -------------------- | ---------------- |
+| `--conda`            | `--enable_conda` |
+| `--clusterOptions`   |                  |
+| `--publish_dir_mode` |                  |
 
 > **NB:** Parameter has been **updated** if both old and new parameter information is present.
 > **NB:** Parameter has been **added** if just the new parameter information is present.

diff --git a/docs/output.md b/docs/output.md
@@ -14,7 +14,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 - [FastQC](#fastqc) - read quality control
 - [TrimGalore](#trimgalore) - adapter trimming
-- [Bowtie2](#bowtie2) - contamination filtering 
+- [Bowtie2](#bowtie2) - contamination filtering
 - [Bowtie](#bowtie) - alignment against mature miRNAs and miRNA precursors (hairpins)
 - [SAMtools](#samtools) - alignment result processing and feature counting
 - [edgeR](#edger) - normalization, MDS plot and sample pairwise distance heatmap

diff --git a/docs/usage.md b/docs/usage.md
@@ -42,12 +42,13 @@ If `MirGeneDB` should be used instead it needs to be specified using `--mirGeneD
 ### Contamination filtering
 
 Contamination filtering of the sequencing reads is optional and can be invoked using `filter_contamination`. FASTA files with contamination sequences to use need to be supplied, otherwise the contamination filtering of the specific type will be omitted. using the following commands:
-- `rrna`: Used to supply a FASTA file containing rRNA conatminations sequence. 
+
+- `rrna`: Used to supply a FASTA file containing rRNA conatminations sequence.
 - `trna`: Used to supply a FASTA file containing tRNA conatminations sequence. e.g. `http://gtrnadb.ucsc.edu/genomes/eukaryota/Hsapi38/hg38-tRNAs.fa`
-- `cdna`: Used to supply a FASTA file containing cDNA conatminations sequence. e.g. `ftp://ftp.ensembl.org/pub/release-86/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz` The FASTA file is first compared to the available miRNA sequences and overlaps are removed. 
-- `ncrna`: Used to supply a FASTA file containing ncRNA conatminations sequence. e.g. `ftp://ftp.ensembl.org/pub/release-86/fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz` The FASTA file is first compared to the available miRNA sequences and overlaps are removed. 
-- `pirna`: Used to supply a FASTA file containing piRNA conatminations sequence. e.g. The FASTA file is first compared to the available miRNA sequences and overlaps are removed. 
-- `other_contamination`: Used to supply an additional filtering set. The FASTA file is first compared to the available miRNA sequences and overlaps are removed. 
+- `cdna`: Used to supply a FASTA file containing cDNA conatminations sequence. e.g. `ftp://ftp.ensembl.org/pub/release-86/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz` The FASTA file is first compared to the available miRNA sequences and overlaps are removed.
+- `ncrna`: Used to supply a FASTA file containing ncRNA conatminations sequence. e.g. `ftp://ftp.ensembl.org/pub/release-86/fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz` The FASTA file is first compared to the available miRNA sequences and overlaps are removed.
+- `pirna`: Used to supply a FASTA file containing piRNA conatminations sequence. e.g. The FASTA file is first compared to the available miRNA sequences and overlaps are removed.
+- `other_contamination`: Used to supply an additional filtering set. The FASTA file is first compared to the available miRNA sequences and overlaps are removed.
 
 ## Samplesheet input