Nextflow: Script of python don't save output

Question

I have problem with a script of Python in Nextflow, my aim is write a file in the script of python and take this with nextflow and save the file in the publishdir (and after I use this file in other process). My process in nextflow is something like this (the files were defined before):

process writefile{
publishDir "${params.output_dir}/formatted", mode: 'copy'
input:
path file from change_file
output:
path "formattedfile.txt" into file_changed
script:
"""
file2formattedfile.py ${file} formattedfile.txt
"""
}

The script of python: (I simplified the real process, but essentiality is something like this), I need obtain in nextflow the file save in output file.

#!/usr/bin/env python3
import argparse
from sys import argv
def main():
   input,output = argv[1:3] 
   out = open(output, "w") 
   #My real operations are here
   out.write("Operations and text") 
   out.close() 

if __name__ == "__main__":
   main()

The problem is the file is don't save in the publish dir, but is in the dir work of nextflow, when i run the workflow the process is completed without error but said DataflowQueue(queue=[])

[e1/74e0ee] process > writefile (DataflowQueue(queue=[])) [100%] 1 of 1 ✔

Thanks!

------------- Update -------------

I changed the input file to a file(). The nextflow.config:

params {
  input_file = 'data/old_file.txt'
  output_dir = 'output_new'
}

The main.nf

change_file = file(params.input_file)
process writefile{
publishDir "${params.output_dir}/formatted", mode: 'copy'
input:
path file from change_file
output:
path "formattedfile.txt" into file_changed
script:
"""
file2formattedfile.py ${file} formattedfile.txt
"""
}

This changed the ouptput of nextflow, but my input file wasn't in the publish dir (but is in the dir work).

[7d/78559b] process > writefile (/home/myuser/Documentos/dir/pipeline_dir/data/old_file.txt) [100%] 1 of 1 ✔

This path after writefile is the path where is my input file, I don't know why (nothing is change in this dir).

Answer 1

Looks like something is wrong with your input using the 'change_file' channel. If 'change_file' should be a value channel, consider the following:

params.change_file = 'my_change_file.txt'
params.output_dir = 'my_output_dir'

change_file = file(params.change_file)


process writefile{

    publishDir "${params.output_dir}/formatted", mode: 'copy'

    input:
    path infile from change_file

    output:
    path "formattedfile.txt" into file_changed

    """
    file2formattedfile.py "${infile}" formattedfile.txt
    """
}

Results:

[d6/5173c1] process > writefile [100%] 1 of 1 ✔

If the above doesn't help, please show how the 'change_file' channel is being created.