I have a process generating two files that I am interested in, hitsort.cls and contigs.fasta. I output these using publishdir:
process RUN_RE {
publishDir "$baseDir/RE_output", mode: 'copy'
input:
file 'interleaved.fq'
output:
file "${params.RE_run}/seqclust/clustering/hitsort.cls"
file "${params.RE_run}/contigs.fasta"
script:
"""
some_code
"""
}
Now, I need these two files to be an input for another process but I don't know how to do that.
I have tried calling this process with
NEXT_PROCESS(params.hitsort, params.contigs)
while specifying the input as:
process NEXT_PROCESS {
input:
path hitsort
path contigs
but it's not working, because only the basename is used instead of the full path. Basically what I want is to wait for RUN_RE to finish, and then use the two files it outputs for the next process.
Best to avoid accessing files in the publishDir, since:
The recommendation is therefore to ensure your processes only access files in the working directory, (i.e.
./work
). What this means is: it's best to avoid things like absolute paths in your input and output declarations. This will also help ensure your workflows are portable.The above workflow block is effectively the same as: