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Update pipelines.md #22

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6 changes: 3 additions & 3 deletions docs/pipelines.md
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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