README.md

NF-E2P2

NextFlow pipeline to run E2P2 software (versions 3 or 4) in batch mode.

INSTALL

E2P2 Singularity/Apptainers are automatically downloaded, no installation need (except Singularity and NextFlow).

You need to install:

• wget
• gzip
• NextFlow (> 21.04.0) (Java 8 or later is required) : https://www.nextflow.io/index.html#GetStarted
• Singularity container app (> 3.0) : https://sylabs.io/guides/3.0/user-guide/index.html

Usage

./nf-e2p2.sh --help

#Load mandatory modules/environment (Singularity & NextFlow)

Usage:
./nf-e2p2.sh [--parameters] [--slurm] --proteome <FULL path to fasta file> [ --e2p2_version <3 or 4> ]

#more details
./nf-e2p2.sh --parameters

#each parameter can be overwritten using command line syntax (--param) or adding it in config file

# --slurm parameter disables nohup/background submission which is incompatible with sbatch submission

Run output directory

runs
└── <SEQNAME>-<RUNHASH>
    ├── logs
    ├── work
    ├── singularity
    └── results

• RUNHASH is computed with sequence file content en config file content (command line are not taken into account)
• singularity directory contains aumatically retrieved containers (from https://lipm-browsers.toulouse.inra.fr/pub/singularity-repository/functional_annotation/ )
• work directory contains task directories - WARNING : can become huge in size
• results directory contains final files

Results output subdirectories

Directory	Content
${proteome}	E2P2 result file
08_pipeline_info	Execution timeline, resources usage, softwaresersions

Results output files

$outdir
├── 08_pipeline_info
│   ├── execution_report.html
│   ├── execution_timeline.html
│   ├── execution_trace.txt
│   └── pipeline_dag.svg
└── ${proteome}
    ├── ${proteome}.e2p2v${e2p2_version}
    ├── ${proteome}.e2p2v${e2p2_version}.long
    ├── ${proteome}.e2p2v${e2p2_version}.orxn.pf
    └── ${proteome}.e2p2v${e2p2_version}.pf

Contact

[email protected]

Credits

• Sébastien Carrere
• Ludovic Cottret

Citations

• https://github.com/carnegie/E2P2
• Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316–319. doi:10.1038/nbt.3820
• Kurtzer GM, Sochat V, Bauer MW (2017) Singularity: Scientific containers for mobility of compute. PLOS ONE 12(5): e0177459. https://doi.org/10.1371/journal.pone.0177459