https://github.com/dgrfs/nfcore_rnaseq_cardiff_university_hawk
RNA Sequencing pipeline on Cardiff University Hawk using NF-Core with example data.
https://github.com/dgrfs/nfcore_rnaseq_cardiff_university_hawk
nextflow nf-core rna-seq-pipeline
Last synced: 3 months ago
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RNA Sequencing pipeline on Cardiff University Hawk using NF-Core with example data.
- Host: GitHub
- URL: https://github.com/dgrfs/nfcore_rnaseq_cardiff_university_hawk
- Owner: dgrfs
- License: mit
- Created: 2024-06-28T22:58:26.000Z (11 months ago)
- Default Branch: main
- Last Pushed: 2024-07-20T13:03:28.000Z (10 months ago)
- Last Synced: 2025-01-07T17:45:53.295Z (5 months ago)
- Topics: nextflow, nf-core, rna-seq-pipeline
- Language: Shell
- Homepage: https://dgrfs.github.io/NFCore_RNASeq_Cardiff_University_Hawk/
- Size: 22.1 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# RNASeq NF-Core pipeline setup
[](https://orcid.org/0009-0001-5312-511X)
[](https://doi.org/10.5281/zenodo.10740117)
[Example data source](https://github.com/hartwigmedical/testdata)
[NF-CORE RNASeq processing pipeline v3.12.0](https://nf-co.re/rnaseq/3.12.0)
Dependencies (available modules on HPC)
- Nextflow Tools
- Singularity
- TMUX
## Getting started
```
git clone https://dgrfs.github.io/NFCore_RNASeq_Cardiff_University_Hawk/
```
## Download genome reference files
Get reference files (OPTIONAL, but improves reproducibility and saves time)
This may take some time depending on server demand
```
cd ref
bash get-refs.sh
# back to working directory when download is complete
cd ..
```
Base config file for SCW can be found: https://nf-co.re/configs/scw
Note options on the scw config README for moving particular processes to 'highmem' partition (required if using HISAT2)
## Set up environment
```
# set up screen/tmux to run in background
module load tmux
tmux
```
```
# load dependencies
module load singularity-ce/3.11.4
module load nextflow/22.10.6
```
## Run Nextflow pipeline
```
nextflow run nf-core/rnaseq \
-r 3.12.0 \
-params-file params.yaml \
-profile singularity \
-c adapted.scw.config \
--fasta $PWD/ref/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz \
--gtf $PWD/ref/Homo_sapiens.GRCh38.108.gtf.gz
```
## OPTIONAL: Faster startup with saved references
Nextflow builds references. If you are running the pipeline multiple times, to speed up the process you can set save_reference to TRUE in params.yaml, and then refer to those saved references in future runs.
After references have been made in the first run, add the following to params.yaml (change PATH to your references where appropriate):
```
fasta: $PWD/ref/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz
gtf: $PWD/ref/Homo_sapiens.GRCh38.108.gtf.gz
hisat2_index: $PWD/ref/genome/index/hisat2
gen_bed: $PWD/ref/genome/Homo_sapiens.GRCh38.108.bed
transcript_fasta: $PWD/ref/genome/genome.transcripts.fa
splicesites: $PWD/genome/index/Homo_sapiens.GRCh38.108.splice_sites.txt
rsem_index: $PWD/ref/genome/rsem
salmon_index: $PWD/ref/genome/index/salmon
```
## FAQ:
### I have multiple SLURM accounts. How do I specify which SLURM account to charge to?
Nextflow uses your default SLURM account to charge jobs to.
To find out SLURM accounts you are a member of, run the following command:
```
sacctmgr show user withassoc \
format=account,user,defaultaccount where user=$USER
```
On the adapted.scw.config file, uncomment the clusterOptions command, and change [MY_ACCOUNT_NAME] to the account you would like to charge to.
### How do I run a local pipeline with a static version of nf-core/rnaseq?
In working directory, get a specific version (look at tags on nf-core/rnaseq for the version you want. In this, we have downloaded version 3.12.0)
```
git clone --branch 3.12.0 https://github.com/nf-core/rnaseq
```
The run nr-core rnaseq nextflow with the following command
```
nextflow run rnaseq/main.nf \
-params-file params.yaml \
-profile singularity \
-c adapted.scw.config \
--fasta $PWD/ref/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz \
--gtf $PWD/ref/Homo_sapiens.GRCh38.108.gtf.gz
```