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Pipeline deployment with geniac

The geniac module allows the automatic generation of the Nextflow configuration files (including profiles) and the container recipes and their creation.

Prerequisite

  • git (>= 2.0) [required]
  • cmake (>= 3.0) [required]
  • Nextflow (>= 20.01) [required]
  • Singularity (>= 3.2) [optional]
  • Docker (>= 18.0) [optional]

First, the user can defined the following environment variables:

#!/usr/bin/env bash
export WORK_DIR=/data/tmp/$USER/sandbox/nf-CRISPR
export SRC_DIR=$WORK_DIR/src
export INSTALL_DIR=$WORK_DIR/install
export BUILD_DIR=$WORK_DIR/build

Initialization

Using the default behavior, only the installation folder where the pipeline will be deployed is required through the CMAKE_INSTALL_PREFIX option.

git clone --recursive https://gitlab.curie.fr/data-analysis/nf-CRISPR $SRC_DIR
mkdir -p $INSTALL_DIR $BUILD_DIR
cd $BUILD_DIR
cmake $SRC_DIR/geniac -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR

The cmake command can be used with the following options ;

  • ap_annotation_path: Path to the annotation folder used by the pipeline. ("")
  • ap_install_docker_images: Build the docker containers ("OFF")
  • ap_install_docker_recipes: Generate the docker recipes ("OFF")
  • ap_install_singularity_images: Build the singularity containers ("OFF")
  • ap_install_singularity_recipes: Gene the singularity recipes ("OFF")
  • ap_nf_executor: Cluster scheduler used by Nextflow ("pbs")
  • ap_singularity_image_path: Path to the singularity containers ("")
  • ap_use_singularity_image_link: Use path to the singularity images ("OFF")

Example

In the following example, the singularity images are available in the SING_DIR folder, and will thus be used during the deployment of the pipeline using the options ap_singularity_image_path et ap_use_singularity_image_link.

cmake $SRC_DIR/geniac -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -Dap_singularity_image_path="${SING_DIR}" -Dap_use_singularity_image_link="ON"

Installation

Note that if the installation of singularity or docker images has been activated at the previous stage, the make command needs to be run with the root rights.

cd $BUILD_DIR
make
make install

Test

Singularity

cd ${INSTALL_DIR}/pipeline  

nextflow run main.nf --singleEnd 'true' --genome 'hg38' --library 'GW-KO-Sabatini-Human-10' --samplePlan 'test/sample_plan.csv' -profile singularity

Multiconda

The multiconda profile generates a conda environment for each tool listed in the conf/geniac.conf configuration.

cd ${INSTALL_DIR}/pipeline  

nextflow run main.nf --singleEnd 'true' --genome 'hg38' --library 'GW-KO-Sabatini-Human-10' --samplePlan 'test/sample_plan.csv' -profile multiconda