fix linting errors with prettier

README.md

@@ -45,13 +45,13 @@ with `-profile test` before running the workflow on actual data.
 
 Now, you can run the pipeline using:
 
-   ```bash
-   nextflow run /path/to/clonedrepo/main.nf \
-     --input samplesheet.csv \
-     --outdir <OUTDIR> \
-     --genome GRCh37 \
-     -profile singularity
-   ```
+```bash
+nextflow run /path/to/clonedrepo/main.nf \
+  --input samplesheet.csv \
+  --outdir <OUTDIR> \
+  --genome GRCh37 \
+  -profile singularity
+```
 
 :::warning
 Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those

docs/output.md

@@ -81,7 +81,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 </details>
 
-[featureCounts]([https://htseq.readthedocs.io/en/master/htseqcount.html](https://subread.sourceforge.net/featureCounts.html)) takes a file with aligned sequencing reads, plus a list of genomic features and counts how many reads map to each feature.
+[featureCounts](https://subread.sourceforge.net/featureCounts.html) takes a file with aligned sequencing reads, plus a list of genomic features and counts how many reads map to each feature.
 
 [Kallisto](http://pachterlab.github.io/kallisto/) quantifies abundances of transcripts from RNA-Seq data using high-throughput sequencing reads.
 

docs/usage.md

@@ -65,7 +65,8 @@ the following is a description of each field that can be used. Fields that do no
 #### UMI
 
 FORTE can extract and deduplicate samples with either single or dual UMI. These functions can be turned on by using the `umi` and `umi2` columns in the samplesheet and entering UMI patterns in one of two ways:
-1. The string method that is described by [UMI-tools](https://umi-tools.readthedocs.io/en/latest/reference/extract.html#extract-method) (e.g. `NNNXX`). 
+
+1. The string method that is described by [UMI-tools](https://umi-tools.readthedocs.io/en/latest/reference/extract.html#extract-method) (e.g. `NNNXX`).
 2. A number, which will indicate the number of bases to be extracted from the beginning of the respective read (e.g. `3`).
 
 The fusion workflows of FORTE will use UMI-extracted reads, where applicable, but not deduplicated reads. The final BAM produced by FORTE is deduplicated where applicable, and by default the expression counts are based on deduplicated BAMs.