usage.md

Run pipeline

When you have installed the pipeline, created a design file and configured the pipeline you can run it with the command line.

With a parameter file

If you want to run the workflow with a parameter file the command is:

$ nextflow run main.nf -params-file examples/params/single_end.yml

, or:

$ nextflow run main.nf -params-file examples/params/paired_end.yml

With command line arguments

The native Nextflow's command line arguments are preceded by -, for example -params-file. However, the nextflow command accepts any parameter if it is preceded by --. You can also specify parameters at the command-line to override those provided in the config files. A list of these can be obtained with:

$ nextflow run main.nf --help

For example, the genome_version parameters can be passed to nextflow like this:

$ nextflow run main.nf --genome_version GRCh38

Thus, in this way, all the parameters of the pipeline can be passed via a shell script:

$ nextflow run main.nf --genome_version GRCh38 --genome_release 86 --strandedness none --design examples/designs/single_end.csv --conda /camp/stp/babs/working/software/anaconda/envs/rnaseq_pipeline

, or:

$ nextflow run main.nf --genome_version GRCh38 --genome_release 86 --strandedness none --design examples/designs/paired_end.csv --conda /camp/stp/babs/working/software/anaconda/envs/rnaseq_pipeline