use same output in two processes in nextflow dsl2

Question

This is my workflow:

pre_align()
pre_align.out.single_fastqs.view()
get_fq_info(pre_align.out.single_fastqs)
align_bwa(get_fq_info.out.fq_info)
align_bowtie2(get_fq_info.out.fq_info)

where I want to use the same output from get_fq_info as input for either align_bwa and align_bowtie2`.

As it's shown here only align_bwa is executed. If I comment align_bwa THEN align_bowtie2 gets executed.

How can I fix this?

Thank you!

Answer 1

I have solved this problem in the past by duplicating the output channel of the desired process in order to feed the same output into multiple downstream processes.

Answer 2

As far as I know, DSL2 should be able to handle this. Have you specified an output qualifier for your process get_fq_info (e.g. path)? I ran into a similar issue when I forgot to specify it.

For example, this will result in the error process align_bowtie2 declares 1 input channel but 0 were specified:

process get_fq_info {
   input:
   path reads
output:
   "output.txt"
shell:
   """
   myprocess.sh ${reads} > output.txt
   """
}

And is probably solved by this:

process get_fq_info {
   input:
   path reads
output:
   path "output.txt"
shell:
   """
   myprocess.sh ${reads} > output.txt
   """
```