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?
nextflow
asked Nov 23 '18 at 16:40
Adam BellaïcheAdam Bellaïche
105
add a comment |
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?
nextflow
asked Nov 23 '18 at 16:40
Adam BellaïcheAdam Bellaïche
105
add a comment |
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?
nextflow
asked Nov 23 '18 at 16:40
Adam BellaïcheAdam Bellaïche
105
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?
nextflow
nextflow
asked Nov 23 '18 at 16:40
Adam BellaïcheAdam Bellaïche
105
asked Nov 23 '18 at 16:40
Adam BellaïcheAdam Bellaïche
105
edited Nov 23 '18 at 17:07
Adam Bellaïche
asked Nov 23 '18 at 16:40
Adam BellaïcheAdam Bellaïche
105
asked Nov 23 '18 at 16:40
Adam BellaïcheAdam Bellaïche
105
asked Nov 23 '18 at 16:40
Adam BellaïcheAdam Bellaïche
105
105
add a comment |
add a comment |
1 Answer
1
active
oldest
votes
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
answered Nov 24 '18 at 18:55
pditommasopditommaso
1,05021429
add a comment |
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1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
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
answered Nov 24 '18 at 18:55
pditommasopditommaso
1,05021429
add a comment |
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
answered Nov 24 '18 at 18:55
pditommasopditommaso
1,05021429
add a comment |
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
answered Nov 24 '18 at 18:55
pditommasopditommaso
1,05021429
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
answered Nov 24 '18 at 18:55
pditommasopditommaso
1,05021429
answered Nov 24 '18 at 18:55
pditommasopditommaso
1,05021429
answered Nov 24 '18 at 18:55
pditommasopditommaso
1,05021429
answered Nov 24 '18 at 18:55
pditommasopditommaso
1,05021429
1,05021429
add a comment |
add a comment |
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