Skip to content

Added clean intermediate files section to README #225

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
apeltzer merged 1 commit into from
Jun 25, 2019
Merged

Added clean intermediate files section to README #225

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 6 additions & 0 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -66,6 +66,12 @@ nextflow run nf-core/eager -profile <docker/singularity/conda>,test --pairedEnd
nextflow run nf-core/eager -profile <docker/singularity/conda> --reads'*_R{1,2}.fastq.gz' --fasta '<REFERENCE>.fasta'
```

6. Once your run has completed successfully, clean up the intermediate files.

```bash
nextflow clean -k
``

NB. You can see an overview of the run in the MultiQC report located at `<OUTPUT_DIR>/MultiQC/multiqc_report.html`

Modifications to the default pipeline are easily made using various options
Expand Down
⚡