Same files order

[giusmar]

Hi, i started to work on nextflow recently, with DSL2.0, so i've some little problem.
I'm trying to build up a simple nextflow pipeline for RNA seq and i link file in a reads.yml file that i put in the pipeline with -params-file.
In the reads.yml i configure the reads as:

reads:
- - name_of_read_one
  - ['/absolute/path/to/read_one', '/absolute/path/to/read_two' ]
- - name_of_read_two
  - ['/absolute/path/to/read_one', '/absolute/path/to/read_two' ]

and in a specific step, i need to include the ouput of a previous process and the reads parameteres in the workflow as:

workflow bar {
   take:
    reads
   
   main:
    umitools(reads) //to extract umi
    foo(reads, umitools.out) //to remove umi with trim galore
}

The problem is that in the foo module, the reads file and processed file from umitools have not the same order, so when trim galore had to remove umi in the second read, it can be different so the process stopped. Is like the processed read of name_of_read_one is setted in analysis with name_of_read_two read.

Can you sugget me how can i avoid this isssue? It's a problem my main.nf pipeline, i don't think that you need my software versions.

[giusmar]

Hi,
for now i ve resolved the issue (for me) creating a new channel in which i merge data from first two process for the third one.

Example:

foo(reads)
unit = bar.out.join(reads)
bar(unit)

For now i'm not sure that i've completely resolved the problem. I ll update this 3d as soon as possible if the pipeline will output goods files.

bye,a
GM