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Nextflow

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Using a "regular" NextFlow workfow#

wget https://github.com/nf-core/configs/blob/master/conf/ifb_core.config
module load nextflow slurm-drmaa graphviz

# Or let nf-core client download the workflow
srun nextflow run ... -profile ifb_core.config ...

# To launch in background
sbatch --wrap "nextflow run ... -profile ifb_core.config ..."

Functional annotation with Orson pipeline#

Orson is a functional annotation pipeline developed in Nextflow by the SeBiMERteam and available at this address : https://gitlab.ifremer.fr/bioinfo/workflows/orson/-/tree/master

# Clone repository 
git clone https://gitlab.ifremer.fr/bioinfo/workflows/orson.git

You might at first run the pipeline with test dataset:

module load nextflow graphviz

# Get the config file for your cluster
wget https://raw.githubusercontent.com/nf-core/configs/master/conf/ifb_core.config -O orson/conf/ifb_core.config

# Run Orson with test dataset
cd orson/
srun nextflow run main.nf -profile test,singularity --downloadDB_enable false \
--hit_tool=diamond --blast_db "/path/to/indexed/db" \
-c conf/ifb_core.config -resume

The test dataset will be imported and then multiple analysis will be run:

  • EggNOG-Mapper
  • InterProScan
  • BeeDeem
  • Busco
  • Diamond

Once you know it works well, you can run analysis with your own dataset:

Here an example of sbatch file : 

#!/bin/bash
#SBATCH -p long

module load nextflow graphviz

nextflow run main.nf --fasta "query.fa" --query_type p -profile custom,singularity --downloadDB_enable false \
--blast_db "/path/to/indexed/db" -c conf/ifb_core.config -resume

By default, the previous tools will be launched, but it is possible to disable some of them.

There are some useful arguments :

--query_type [n,p]

Set to "n" for nucleic acid sequences input or to "p" for protein sequences.

--hit_tool [PLAST, BLAST, diamond]

Indicates the tool of your choice for the comparison of your sequences to the reference database.

--outdir

The output directory where the results will be published.

-w/--work-dir

The temporary directory where intermediate data will be written. (Can be /scratch/ directory)

Please refere as Orson's documentation for more details : https://gitlab.ifremer.fr/bioinfo/workflows/orson/-/tree/master/docs

Note that Orson will check the presence of Singularity containers in orson/container/ and if it doesn't find it, it will import them.

Using nf-core#

All nf-core pipelines have been successfully configured for use on the ABiMS cluster.

Check this page: github.com/nf-core/configs/blob/master/docs/ifb_core.md