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nextflow

Data-driven computational pipelines

Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.

Options

Version based on distribution from https://www.nextflow.io

Defaults for build are

  • NEXTFLOW_VERSION=0.30.1
  • LMOD_MODULE_DIR=/opt/apps/Linux

Other dependencies

Java - java module build

Build

docker image

Build docker image from the java/ directory

docker build -t lmod.nextflow .

Lmod package files and Lua script

Generate the Lmod package files and Lua script by running the container with optional environment variable overrides for NEXTFLOW_VERSION and LMOD_MODULE_DIR.

The output files will be saved to the directory mapped to the /output volume of the container. For clarity this should map to the version of the package being generated.

Example:

docker run --rm \
  -v $(pwd)/0.30.1:/output \
  -e NEXTFLOW_VERSION=0.30.1 \
  -e LMOD_MODULE_DIR=/opt/apps/Linux \
  lmod.nextflow

Upon completion the following files should be observed

$ ls -lh $(pwd)/0.30.1
total 56696
-rw-r--r--  1 stealey  staff   393B Jun 12 12:44 0.30.1.lua
-rw-r--r--  1 stealey  staff    28M Jun 12 12:44 nextflow-0.30.1.tar.gz

Install

The generated files should be placed into the target systems modules (/opt/apps/Linux) and modulefiles (/opt/apps/modulefiles/Linux) directories using the hierachy:

  • Modules: /opt/apps/Linux/nextflow/nextflow-0.30.1
  • Modulefiles: /opt/apps/modulefiles/Linux/nextflow/0.30.1.lua

Example installation

  • Where modules and modulefiles directories are mapped to the target systems /opt/apps/Linux and /opt/apps/modulefiles/Linux directories respectively.
  • Assumes lmod-modules-centos repository is one level up for relative path commands.
mkdir -p modules/nextflow
mkdir -p modulefiles/nextflow
cp ../lmod-modules-centos/nextflow/0.30.1/nextflow-0.30.1.tar.gz \
  modules/nextflow/nextflow-0.30.1.tar.gz
cp ../lmod-modules-centos/nextflow/0.30.1/0.30.1.lua \
  modulefiles/nextflow/0.30.1.lua
cd modules/nextflow
tar -xzf nextflow-0.30.1.tar.gz
rm -f nextflow-0.30.1.tar.gz
cd -

module avail

Once installed Lmod will show the module as:

$ module avail

-------- /opt/apps/modulefiles/Linux --------
   java/1.8.0_171    nextflow/0.30.1
  • NOTE: java/1.8.0_171 is also shown due to it being a nextflow dependency