How to save the multiple output of single process in publishDir in Nextflow - nextflow

Question

I have the process create_parallel_params whose output is parallel_params folder containing json files.
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
params.spectra = "$baseDir/data/spectra/"
params.library = "$baseDir/data/library/"
params.workflow_parameter="$baseDir/data/workflowParameters.xml"
TOOL_FOLDERS="$baseDir/bin"
process create_parallel_params{
publishDir "$baseDir/nf_output", mode: 'copy'
output:
path "parallel_params/*.json"
script:
"""
mkdir parallel_params | python $TOOL_FOLDERS/parallel_paramgen.py \
parallel_params \
10
"""
}
The output of the above process passed into process searchlibrarysearch_molecularv2_parallelstep1 which process each json file.
process searchlibrarysearch_molecularv2_parallelstep1{
publishDir "$baseDir/nf_output", mode: 'copy'
input:
path json_file
//path params.spectra
//path params.library
output:
path "result_folder" emit:"result_folder/*.tsv"
script:
"""
mkdir result_folder convert_binary librarysearch_binary | \
python $TOOL_FOLDERS/searchlibrarysearch_molecularv2_parallelstep1.py \
$params.spectra \
$json_file \
$params.workflow_parameter \
$params.library \
result_folder \
convert_binary \
librarysearch_binary \
"""
}
workflow{
ch_parallel_params=create_parallel_params()
ch_searchlibrarysearch=searchlibrarysearch_molecularv2_parallelstep1(create_parallel_params.out.flatten())
ch_searchlibrarysearch.view()
}
I want the output of these file in publishDir (nf_output) in a single folder. So How can i do that. Provide some example.

Answer 1

The emit option can be used to assign a name identifier to an output channel. This is helpful if your output declaration defines more than one output channels, but isn't usually necessary if you make only a single declaration. Providing a glob pattern as an identifier doesn't make much sense: if you need only the output TSV files (and not the whole folder), you can just use the following and the output TSV files will be published to the publishDir:
output:
path "result_folder/*.tsv"
If you want to declare the folder itself, usually you can just update your publishDir to include a subdirectory with a unique name. You could use something like:
publishDir "$baseDir/nf_output/${json_file.baseName}", mode: 'copy'
But this will give you a 'result_folder' in every subdirectory. If that's not desirable, it might be preferable to change your output declaration to:
output:
path "result_folder/*"