docs: additional changes

CCBR · Nov 21, 2024 · c9f9e70 · c9f9e70
1 parent cd80d3d
commit c9f9e70
Showing 1 changed file with 3 additions and 0 deletions.
diff --git a/docs/user-guide/pipeline.md b/docs/user-guide/pipeline.md
@@ -115,8 +115,11 @@ Example of Tumor only calling mode
 ```bash
 # preview the logan jobs that will run 
 nextflow run LOGAN/main.nf --mode local -profile ci_stub --genome hg38 --outdir out --fastq_input "*R{1,2}.fastq.gz" --callers octopus,mutect2 -preview --vc --sv --cnv
+
 # run a stub/dryrun of the logan jobs 
+
 nextflow run LOGAN/main.nf --mode local -profile ci_stub --genome hg38 --outdir out --fastq_input "*R{1,2}.fastq.gz" --callers octopus,mutect2 -stub --vc --sv --cnv
+
 # launch a logan run on slurm with the test dataset
 nextflow run LOGAN/main.nf --mode slurm -profile biowulf,slurm --genome hg38 --outdir out --fastq_input "*R{1,2}.fastq.gz" --callers octopus,mutect2 --vc --sv --cnv
 ```