Modifying Parameters
Pipeline specific parameters can be found in nextflow.config
| Retuired Parameters | Description |
|---|---|
| inputdir | The folder that contains the input files (default ‘data’) |
| outputdir | The folder where you want the resulting data to be saved (default ‘results/results’) |
| Optional Parameters | Description |
|---|---|
| qc_only | If enabled, only QC workflow is run (default ‘false’) |
| gvcf_only | If enabled, only gVCF workflow is run (default ‘false’) |
| trim_adapter | The adapter used for initial trimming of reads (default ‘NexteraPE-custom.fa’) |
Some common nextflow parameters
| Nextflow Parameters | Description |
|---|---|
| -profile | allows you to select a specific configuration profile defined in your Nextflow configuration files |
| -work-dir | specifies the directory where Nextflow will store intermediate files and results |
| -config | allows you to specify an additional configuration file |
Notice how there some parameters have two hypens in front of their name (ie. --inputdir) and some only have one (ie. -profile). The difference is because some parameters are pipeline-specific while others are defined by nextflow. Two hyphens (‘–’) indcate that the parameter is defined within the pipeline, and a single hypen (-) indicates that the parameter is nextflow defined.
Example
Below is an example of how you may use the above parameters on the command line:
Running QC Only with different trim adapters (default is a custom Nextera adapter) by adding –qc_only and –trim_adapter parameters as well as nextflow -workdir parameter
nextflow run main.nf \
-work-dir path/work \
-profile sge,apptainer \
--inputdir path/input_directory_fastq \
--outputdir path/output_directory \
--trim_adapter path/adapters/TruSeq2-PE.fa
--qc_only true