nextflow-training
Run some examples
$ nextflow run combineInput.nf -resume -process.echo
$ nextflow run inputRepeaters.nf -resume -process.echo
How to use containers with nextflow
Create a file nextflow.config (mind '' for delimiting the paramters):
process.container='nextflow/rnaseq-nf'
docker.runOptions='-u $(id -u):$(id -g)'
Pull a docker image:
$ docker pull nextflow/rnaseq-nf
Then call nextflow with with-docker parameter:
$ nextflow run script2.nf -with-docker
Adding:
docker.enabled=true
to nextflow.config let to avoid specifing -with-docker parameter when calling nextflow
Override parameters using cmd
Override the default reads parameter:
$ nextflow run script3.nf --reads 'data/ggal/*_{1,2}.fq' -resume
Calling:
$ nextflow run script4.nf
$ nextflow run script4.nf -resume --reads 'data/ggal/*_{1,2}.fq'
will execute only the new calculations and will re-use the old computed results
Calling a nextflow project using git
calling nextflow on this git repository: https://github.com/nextflow-io/rnaseq-nf.git
$ nextflow run nextflow-io/rnaseq-nf
I can call a specific revison of a nextflow git pipeline. Or by calling:
$ nextflow run rnaseq-nf -with-docker -with-report -with-trace -with-timeline -with-dag dag.png -resume
I can generate some useful reports