To test the workflow simply do
make run [-e --annotations=<annotations_file> --xmlpath=<xmlpath)> --ppm_tolerance=<ppm_tolerance>]
If you do not specify an input file, by default it will take the sample files located in data/annotations.tsv and the mzXML files containing the positive and negative spectra. The default ppm_tolerance is 10.0
Please visit the GNPS documentation for more information about msms-choser.
To learn NextFlow checkout this documentation:
https://www.nextflow.io/docs/latest/index.html
The parameters in nextflow follow the next priority:
i. Parameters specified on the command line (--something value) ii. Parameters provided using the -params-file option iii. Config file specified using the -c my_config option iv. The config file named nextflow.config in the current directory v. The config file named nextflow.config in the workflow project directory vi. The config file $HOME/.nextflow/config vii. Values defined within the pipeline script itself (e.g. main.nf)
In case you wish to set your parameters directly in nextflow, please use the next syntaxis:
nextflow [options] ./nf_workflow.nf --annotations="$(annotations_file)" --path_to_spectra="$(path_to_spectra)" --ppm_tolerance=$(ppm_tolerance) --resume -c nextflow.config
To run the workflow in a conda environment, there is a configuration file conda_env.yml. This file configured the environment named msms-choser-env. It can be created and activated by:
conda env create -f bin/conda_env.yml
conda activate msms-choser-env
and then the workflow can be executed from the conda environment. If you do not specify an input file, by default it will take the sample files located in data/annotations.tsv and the mzXML files containing the positive and negative spectra.
nextflow [options] ./nf_workflow.nf --annotations="$(annotations_file)" --path_to_spectra="$(path_to_spectra)" --ppm_tolerance=$(ppm_tolerance) --resume -c nextflow.config