pre-commit :)

docs/output.md

@@ -169,7 +169,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 The workflow is designed to output three files _per sample_, _per quantification tool_ in the `circrna_discovery` directory. Using the test dataset as an example, the directory structure for the `fust_1` sample is:
 
-```console
+````console
 |-- results/
       |-- circrna_discovery/
             |-- circexplorer2/
@@ -194,7 +194,7 @@ Sample outputs for the corresponding `.log`, `.bed` and `.fasta` entry are given
 [nf-core/circrna]: Attempting to fit circRNA to gene exon boundaries
 [nf-core/circrna]: chrI:1140805-1147588:- fits gene exons, is a circRNA
 [nf-core/circrna]: cleaning up intermediate files
-```
+````
 
 ```console
 chrI	1140805	1147588	chrI:1140805-1147588:-	2	-	1140805	1147588	0	5	229,214,191,141,499	0,1282,2546,4912,6284	circRNA	Y48G8AL.10	NM_001306296,NM_001306297,NM_001306298,NM_001306299	1274
@@ -215,6 +215,7 @@ Intermediate files generated by each quantification tool are described in depth
 <summary>Output files</summary>
 
 - `circrna_discovery/circexplorer2/intermediates/${sample_id}/`
+
   - `*.bed`: Intermediate file generated by `CIRCexplorer2 parse` module, identifying STAR fusion junctions for downstream annotation.
   - `*_circexplorer2_circs.bed`: Filtered BED6 file containing circRNA counts used for count matrix generation.
   - `*.txt`: Output files generated by `CIRCexplorer2 annotate` module, based on BED 12 format containing circRNA genomic location information, exon cassette composition and an additional 6 columns specifying circRNA annotations. Full descriptions of the 18 columns can be found in the `CIRCexplorer2` [documentation](https://circexplorer2.readthedocs.io/en/latest/modules/annotate/#output).
@@ -247,6 +248,7 @@ Intermediate files generated by each quantification tool are described in depth
 <summary>Output files</summary>
 
 - `circrna_discovery/circrna_finder/intermediates/${sample_id}/`
+
   - `*.filteredJunctions.bed`: A bed file with **all** circular junctions found by the pipeline. The score column indicates the number reads spanning each junction.
   - `*.s_filteredJunctions.bed`: A bed file with those junctions in `*.filteredJunctions.bed` that are flanked by GT-AG splice sites. The score column indicates the number reads spanning each junction.
   - `*.s_filteredJunctions_fw.bed`: A bed file with the same circular junctions as in file (b), but here the score column gives the average number of forward spliced reads at both splice sites around each circular junction.