Nextflow run options

Nextflow run command has a lot of options, here are the main useful options :

• configuration

  • -profile Choose a configuration profile pipelines can provide several profiles. With this option you can overload parameters. (see next paragraph)[#nextflow-config]

• execution

  • -resume Execute the script using the cached results, useful to continue executions that were stopped by an error
  • -w, -work-dir Directory where intermediate result files are stored

• trace

  • -with-dag Create pipeline DAG file

  • -with-report Create processes execution html report -> really useful to get execution report on memory and cpu usage in order to calibrate pipeline parameters

  • -with-timeline Create processes execution timeline file

  • -with-trace Create processes execution tracing file

• dependancies

  • -with-conda Use the specified Conda environment package or file (must end with .yml|.yaml suffix)

  • -with-docker Enable process execution in a Docker container

  • -with-singularity Enable process execution in a Singularity container.

  • -without-docker Disable process execution with Docker Default: false

• workflow version

  • -latest Pull latest changes before run Default: false

  • -r, -revision Revision of the project to run (either a git branch, tag or commit SHA number)

Exercise 4 :

• Try the following options and explore the new generated files.

  $ nextflow run tutorial.nf -with-timeline -with-trace -with-report -with-dag
  

  This command will generate following files :

  • trace.txt
  • report.html
  • timeline.html
  • dag.dot

• View trace.txt

• View dag with following command:

  $ display dag.dot
  

• To view html, copy files into your directory ~/public_html. Then with a web browser, visit page http://genoweb.toulouse.inra.fr/~USERNAME/

Here is how to configure you public_html directory:

$ mkdir -p ~/save/public_html; ln -s /save/USERNAME/public_html 
$ chmod a+x /save/USERNAME ; chmod 755 /save/USERNAME/public_html ;