If no config.xml file is found in the current path (working directory), the software takes the default config file from the directory where the applications (jars) are installed.
However, the config.xml file cannot be set in the nextflow config. How is one supposed to set the config parameters for the nextflow pipeline if a path to a custom config.xml file cannot be provided for the pipeline run? As far as I can tell, a config file isn't even coded in the nextflow pipeline.
One cannot simply create a custom config.xml in the working directory as stated in the README (presumably for using the bash version of the pipeline):
If no config.xml file is found in the current path (working directory), the software takes the default config file from the directory where the applications (jars) are installed.
...given that Nextflow stages files in isolated working directories, so the working directory of the Nextflow job itself is not "seen" by jobs (processes) run by the Nextflow job.
The README states:
However, the config.xml file cannot be set in the nextflow config. How is one supposed to set the config parameters for the nextflow pipeline if a path to a custom config.xml file cannot be provided for the pipeline run? As far as I can tell, a config file isn't even coded in the nextflow pipeline.
One cannot simply create a custom config.xml in the working directory as stated in the README (presumably for using the bash version of the pipeline):
...given that Nextflow stages files in isolated working directories, so the working directory of the Nextflow job itself is not "seen" by jobs (processes) run by the Nextflow job.