Skip to content

Latest commit

 

History

History
139 lines (114 loc) · 3.68 KB

Nextflow.md

File metadata and controls

139 lines (114 loc) · 3.68 KB
Raw

Nextflow

A DSL for data-driven computational pipelines http://nextflow.io.

In 2022, Nextflow had a backwards-incompatible change that depreacated an old syntax called DSL1 in favor of the DSL2 syntax. We still provide the old version 21.10.6 in the Nextflow module on deigo. Newer versions are in the Nextflow2 module. To use a DSL1 pipeline with the Nextflow2 module, pass the -dsl1 flag to the nextflow program.

The Nextflow2 module also limits the use of memory by setting the environment variable NXF_OPTS to -Xms500M -Xmx2G. Please contact us or open an issue if you hit the limit.

Installation on deigo

See also https://groups.oist.jp/scs/install-software-your-unit.

Release or edge versions from GitHub

Source: https://github.com/nextflow-io/nextflow

APP=Nextflow2
MODROOT=/bucket/BioinfoUgrp/Other
APPDIR=$MODROOT/$APP
VER=24.10.3
mkdir -p $APPDIR/$VER/bin
cd $APPDIR/$VER
wget https://github.com/nextflow-io/nextflow/releases/download/v${VER}/nextflow-${VER}-dist
mv nextflow-${VER}-dist bin/nextflow
chmod 775 bin/nextflow
mkdir -p $MODROOT/$APP/modulefiles/
cd $MODROOT/$APP/modulefiles/
cat <<'__END__' > $VER.lua
-- Default settings
local modroot    = "/bucket/BioinfoUgrp/Other"
local appname    = myModuleName()
local appversion = myModuleVersion()
local apphome    = pathJoin(modroot, myModuleFullName())

-- Package information
whatis("Name: "..appname)
whatis("Version: "..appversion)
whatis("URL: ".."https://github.com/nextflow-io/nextflow/releases")
whatis("Category: ".."bioinformatics")
whatis("Keywords: ".."pipeline, SLURM")
whatis("Description: ".." Data-driven computational pipelines.")

help([[Nextflow version downloaded from GitHub

See https://www.nextflow.io/ for help.]])

-- Package settings
depends_on("singularity")
depends_on("java-jdk/14")
setenv("NXF_OPTS", "-Xms500M -Xmx2G")
prepend_path("PATH", apphome.."/bin")
__END__

nf-test

Testing framework for Nextflow pipelines (https://www.nf-test.com/).

Installation on deigo

APP=nf-test
MODROOT=/bucket/BioinfoUgrp/Other
APPDIR=$MODROOT/$APP
VER=0.9.2
mkdir -p $APPDIR/$VER/bin
cd $APPDIR/$VER
wget https://github.com/askimed/nf-test/releases/download/v${VER}/nf-test-${VER}.tar.gz
pushd bin
tar xvfz ../nf-test-${VER}.tar.gz
chmod 775 nf-test
chmod 664 nf-test.jar
popd
rm nf-test-${VER}.tar.gz
cd $MODROOT/modulefiles/
mkdir -p $APP
cat <<'__END__' > $APP/$VER.lua
-- Default settings
local modroot    = "/bucket/BioinfoUgrp"
local appname    = myModuleName()
local appversion = myModuleVersion()
local apphome    = pathJoin(modroot, myModuleFullName())

-- Package information
whatis("Name: "..appname)
whatis("Version: "..appversion)
whatis("URL: ".."https://github.com/askimed/nf-test/releases")
whatis("Category: ".."bioinformatics")
whatis("Keywords: ".."pipeline, SLURM")
whatis("Description: ".."Testing framework for Nextflow pipelines.")

help([[nf-test version downloaded from GitHub

See https://www.nf-test.com/ for help.]])

-- Package settings
depends_on("Nextflow2")
prepend_path("PATH", apphome.."/bin")
__END__

nf-core

Python package with helper tools for the nf-core community (https://nf-co.re/docs/nf-core-tools).

To install a new latest version, update the VER variable below and run the commands.

ml purge
ml bioinfo-ugrp-modules Nextflow2
APP=nf-core
MODROOT=/bucket/BioinfoUgrp/Other
APPDIR=$MODROOT/$APP
VER=3.1.0
mkdir -p $APPDIR/$VER/bin
cd $APPDIR/$VER/bin
singularity pull docker://nfcore/tools:$VER
mv tools_${VER}.sif nf-core
cat <<"__END__" > pre-commit
#!/bin/sh
singularity exec nf-core pre-commit "$@"
__END__
chmod 775 pre-commit
cd $MODROOT/$APP/modulefiles/
cp 3.0.2.lua ${VER}.lua