GAZODUC

My DSL2 Nextflow Pipelines used at the Insitut du Thorax/Nantes/France.

Works on my machine

Installation

Glicid Users : you can try to install everything using conda/micromamba but I had a poor experience with this solution

Install java

Install a recent version of openjdk (e.g: jdk-23.0.1) from https://jdk.java.net/23/ , and for example download and expand it into ${HOME}/packages/jdk-23.0.1 ( or look under https://jdk.java.net/archive/ ).

add JDK to your ${PATH}:

export PATH=${HOME}/packages/jdk-23.0.1/bin:${PATH}

set the variable JAVA_HOME

export JAVA_HOME=${HOME}/packages/jdk-23.0.1

Install conda/micromamba

Glicid Users : see https://doc.glicid.fr/GLiCID-PUBLIC/alpha/logiciels.html#_installer_micromamba_sur_glicid

Install nextflow

$ mkdir -p ${HOME}/packages
cd ${HOME}/packages
curl -s https://get.nextflow.io | bash
# make it executable
chmod +x nextflow

create the directories where nextflow will download its libraries:

mkdir -p "/scratch/nautilus/users/${USER}/.nextflow/capsule"

Glicid Users : Prepare a CONDA directory for nextflow:

mkdir -p /micromamba/${USER}/envs/nextflow-envs

Glicid Users : Open ${HOME}/.bash_profile and add the following lines. Adjust the variable according to your installation

export NAUTILUS_SCRATCH=/scratch/nautilus/users/${USER}
# disable nextflow logging because I want one line per job instead of one line per process
export NXF_ANSI_LOG=false
# where to put conda/micromamba stuff
export NXF_CONDA_CACHEDIR=/micromamba/${USER}/envs/nextflow-envs
# if you want to use nf-core, don't connect to the web to check the version
export NFCORE_NO_VERSION_CHECK=1
# nextflow wants to put file here
export CAPSULE_CACHE_DIR=${NAUTILUS_SCRATCH}/.nextflow/capsule
# override NF home in the scratch instead of your home
export NXF_HOME=${NAUTILUS_SCRATCH}/.nextflow
# where to install singularity/apptainer stuff
export NXF_SINGULARITY_CACHEDIR=${NAUTILUS_SCRATCH}/.singularity/cache
export NXF_APPTAINER_CACHEDIR=${NXF_SINGULARITY_CACHEDIR}
export NXF_SINGULARITY_LIBRARYDIR=${NAUTILUS_SCRATCH}/.singularity/lib
export NXF_APPTAINER_LIBRARYDIR=${NXF_SINGULARITY_LIBRARYDIR}
# set java home
export JAVA_HOME=${HOME}/packages/jdk-23.0.1
export PATH=${JAVA_HOME}/bin:${HOME}/packages/nextflow:${PATH}
# the following line was found to be required if you want to use micromamba with nextflow
export PATH=${HOME}/.local/bin:${PATH}

Reload bash, Test your installation of nextflow:

$ nextflow info

nextflow Profiles for GLICID users

https://nextflow.io/docs/latest/config.html#config-profiles

Configuration files can define one or more profiles. A profile is a set of configuration settings that can be selected during pipeline execution using the -profile command line option.

• micromamba : tell nextflow to use micromamba
• GRCh38 : fills required information for the GRCh38 reference
• hs38me : fills required information for the hs38me reference
• hs37d5 : fills required information for the hs37d5 reference
• waves : tell nextflow to use the waves cluster .export SLURM_CLUSTERS=waves should be set.
• nautilus : tell nextflow to use the nautilus cluster .export SLURM_CLUSTERS=nautilus should be set.

Example:

nextflow run -profile 'GRCh38,nautilus` main.nf

Install GAZODUC

git clone https://gitlab.univ-nantes.fr/pierre.lindenbaum/gazoduc-nf.git

Testing

note to self:

generate a test:

nf-test generate workflow subworkflows/parabricks/haplotypecaller/main.nf 
nf-test generate process modules/encode/blacklist/main.nf

nf-test test --profile micromamba --tag=subworkflows/samtools/prepare.one.ref

Author

Pierre Lindenbaum PhD. Institut du Thorax. 44000 Nantes. France.