nextflow (with DSL1)

Nextflow is a workflow system for creating scalable, portable, and reproducible workflows.

Nextflow DSL support change :

• In Nextflow version 22.03.0-edge, DSL2 became the default DSL version.
• In version 22.12.0-edge, DSL1 support was removed.
• Last Nextflow that support DSL1 is v22.10.6

Documentation page : https://www.nextflow.io/docs/latest/

Training / workshop : https://training.nextflow.io/2.1.3/hello_nextflow/01_hello_world/

Start interactive session:

tmatejuk@jumphost-17:~$ srun -c1 --mem=1G --pty bash -l

Use bellow commands to install nextflow

cd /tmp
curl -L https://github.com/nextflow-io/nextflow/releases/download/v22.10.6/nextflow -o "nextflow_dsl1"

chmod +x nextflow_dsl1

mkdir -p $HOME/.local/bin/
mv nextflow_dsl1 $HOME/.local/bin/

Consider adding nexflow_dsl1 location to your shell. In Bash, add export PATH=“$PATH:$HOME/.local/bin” to ~/.bashrc.

Confirm nextflow sucessful instalation.

Check nextflow version

tmatejuk@jumphost-17:~$ srun -c1 --mem=1G --pty bash -l

tmatejuk@node090:~$ nextflow_dsl1 info
  Version: 22.10.6 build 5843
  Created: 23-01-2023 23:20 UTC (24-01-2023 00:20 CEST)
  System: Linux 6.1.0-32-amd64
  Runtime: Groovy 3.0.13 on OpenJDK 64-Bit Server VM 17.0.16+8-Debian-1deb12u1
  Encoding: UTF-8 (ANSI_X3.4-1968)

tmatejuk@node090:~$

tmatejuk@node090:~$ exit
tmatejuk@jumphost-17:~$

Run nextflow

tmatejuk@jumphost-17:~$ srun -c1 --mem=1G --pty bash -l

tmatejuk@node090:~$ nextflow_dsl1 run hello
N E X T F L O W  ~  version 22.10.6
Pulling nextflow-io/hello ...
 downloaded from https://github.com/nextflow-io/hello.git
Launching `https://github.com/nextflow-io/hello` [pensive_kilby] DSL2 - revision: 2ce0b0e294 [master]
executor >  local (4)
[0f/7a78cf] process > sayHello (4) [100%] 4 of 4 ✔
Ciao world!

Bonjour world!

Hello world!

Hola world!


tmatejuk@node090:~$ exit
tmatejuk@jumphost-17:~$