CODEWITHSUNDEEP
nextflow
Adam Bellaïche
Adam Bellaïche

Reputation: 437

How to use file script without specifying the absolute path?

I have this processes:

#!/usr/bin/env nextflow

params.queries = ""
params.db = ""

queries = Channel.fromPath(params.queries)
queries.into { queries_psiblast; queries_pssm }
db = file(params.db)

process PsiBlast {

    input:
    file query from queries_psiblast

    output:
    file top_hits

    """
    psiblast -db $db -query $query -out top_hits
    """
} 

process ParsePsiBlastOut {

    input:
    file top_hits

    output:
    file top_hits2

    """
    python3 psi_blast_output_to_fasta_next.py  $top_hits 
    """
}

I have a problem with the second process, Nextflow doesn't find my python script.

Here is my directory (I'm not in HOME, I'm in project/ . So it's not my "bin" in HOME):

bin/  pipeline_amont.nf

My python script is in bin, like the Nextflow doc says.

But Nextflow seems to search it in work.

How can I say to Nextflow to look for the script in bin?

Upvotes: 2

Views: 1356

Answers (1)

pditommaso
pditommaso

Reputation: 3381

Nextflow automatically adds the project bin directory to the task $PATH, therefore you need to invoke your script as a command without specifying the python interpreter i.e. 

psi_blast_output_to_fasta_next.py

instead of 

python3 psi_blast_output_to_fasta_next.py

Upvotes: 3

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