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Using a "regular" NextFlow workfow:
wget https://github.com/nf-core/configs/blob/master/conf/abims.config module load nextflow slurm-drmaa graphviz # Or let nf-core client download the workflow srun nextflow run ... -profile abims.config ... # To launch in background sbatch --wrap "nextflow run ... -profile abims.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/abims.config -O orson/conf/abims.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/abims.config -resume
The test dataset will be imported and then multiple analysis will be run :
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/abims.config -resume
By default, the previous tools will be launched, but it is possible to disable some of them.
There are some useful arguments :
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.
The output directory where the results will be published.
The temporary directory where intermediate data will be written. (Can be
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.
On the ABIMS cluster, containers are already provided in
We need to give this path to nextflow so it won't download it again.
# Give container's path cd orson/ ln -s /shared/software/singularity/images/nextflow/*.sif containers/
It is also possible to run the pipeline with Hectar annotation's tool (for Heterokontes).
To do it, you need to clone the branch of git repository containing Orson's code adapted with Hectar.
As the code is not published, Orson will not fetch the container Singularity, so it is important to provide it. (It is already provided in the container path above).
# Clone repository git clone --depth 1 --branch hectar_rebased https://gitlab.ifremer.fr/abims-sbr/orson.git # Get container cd orson/ ln -s -s /shared/software/singularity/images/nextflow/*.sif containers/
Then run the same command as before, adding
--hectar_enable true to launch Hectar analysis. (Available only for proteins)
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/abims.md