EGCE/genomeassembler

Introduction

EGCE/genomeassembler is a bioinformatics pipeline that ...

<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->2. Present QC for raw reads (MultiQC)

Installation

Nextflow

If your Java version is >= 17, you can install Nextflow in your $HOME folder using:

bash curl -s https://get.nextflow.io | bash chmod +x nextflow mkdir -p $HOME/.local/bin/ mv nextflow $HOME/.local/bin/ echo "export PATH=$HOME/.local/bin/:$PATH" >> $HOME/.bashrc

[!NOTE] If your Java version is < 17, please refer to this page on how to set-up Nextflow.

[!NOTE] You can also install Nextflow system-wide by moving the nextflow executable to a directory accessible to all users: bash sudo mv nextflow /usr/local/bin/

Apptainer

When running the pipeline of multi-user server or on a cluster, the best practice is to use Apptainer (formerly Singularity).

You can install Apptainer by following these instructions.

In case you encounter the following error when running Apptainer: ERROR : Could not write info to setgroups: Permission denied ERROR : Error while waiting event for user namespace mappings: no event received you may need to install the apptainer-suid package instead of apptainer:

```

Debian / Ubuntu

sudo apt install apptainer-suid

RHEL / CentOS

sudo yum install apptainer-suid

Fedora

sudo dnf install apptainer-suid ```

Docker / Podman / Shifter / Charliecloud

You can also use other container technologies to run the pipeline. See the following instructions to install: * Docker * Podman * Shifter * Charliecloud

[!NOTE] For now, the only one that is tested is Docker. If you encounter any problem, please open an issue.

Micromamba / Conda

This pipeline can be launched with Micromamba (or Conda) too and it has been tested successfully.

Although it is not the best practice, it should work perfectly and it can be very convenient when you cannot run containers (Apptainer, Docker, Podman, ...).

• To install Micromamba in your $HOME folder:

bash "${SHELL}" <(curl -L micro.mamba.pm/install.sh) (or see these instructions).

• To install Miniconda in your $HOME folder, see these instructions.

Running the pipeline

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

csv sample,fastq_1,fastq_2 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz

Each row represents a fastq file (single-end) or a pair of fastq files (paired end).

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Now, you can run the pipeline using:

bash nextflow run EGCE/genomeassembler \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --outdir <OUTDIR>

[!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

EGCE/genomeassembler was originally written by Olivier Coen.

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.