Skip to content

Update pipelines.md #22

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
lpantano merged 1 commit into from
May 22, 2025
Merged

Update pipelines.md #22

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: 3 additions & 3 deletions docs/pipelines.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -164,14 +164,14 @@ To run your data, prepare input file following this [doc](https://nf-co.re/viral
module load jdk/21.0.2-fasrc01
```

Use nextflow at `/n/holylfs05/LABS/hsph_bioinfo/Lab/shared_resources/nextflow`
Use nextflow at `/n/holylfs05/LABS/hsph_bioinfo/Lab/shared_resources/nextflow/nextflow`

Use config file at `/n/holylfs05/LABS/hsph_bioinfo/Lab/shared_resources/nextflow/fas.config`

Example command to run in an interactive job:

```
/n/holylfs05/LABS/hsph_bioinfo/Lab/shared_resources/nextflow run nf-core/rnaseq -profile test,singularity --outdir tmp -c /n/holylfs05/LABS/hsph_bioinfo/Lab/shared_resources/nextflow/fas.config
/n/holylfs05/LABS/hsph_bioinfo/Lab/shared_resources/nextflow/nextflow run nf-core/rnaseq -profile test,singularity --outdir tmp -c /n/holylfs05/LABS/hsph_bioinfo/Lab/shared_resources/nextflow/fas.config
```

For non-test data, this is the head job you need to submit. Copy first the config files and modified as needed:
Expand Down Expand Up @@ -203,7 +203,7 @@ export NXF_SINGULARITY_LIBRARYDIR=/n/holylfs05/LABS/hsph_bioinfo/Lab/shared_reso

OUTPUT=path_to_results

/n/holylfs05/LABS/hsph_bioinfo/Lab/shared_resources/nextflow run nf-core/rnaseq -r 3.14.0 \
/n/holylfs05/LABS/hsph_bioinfo/Lab/shared_resources/nextflow/nextflow run nf-core/rnaseq -r 3.14.0 \
-profile singularity \
-c analysis.config \
-c rnaseq.config \
Expand Down