In Nextflow, Does a process with a channel.fromPath is parallelized?
I have a process in Nextflow with multiple input file from a Channel.FromPath().
Here my script:
params.queries = ""
queries = Channel.fromPath(params.queries) #path to multiple .fasta files
process PsiBlast
input:
file query from queries_psiblast
output:
file top_hits
"""
blastpgp -d $db -i $query -j 2 -C ff.chd.ckp -Q pssm.out >> top_hits
"""
#then there are others processes, not needed for my question.
What I want to know is if my process is parallelized? If it run on 2 files at the same time for example? Or do I need to specify it in my script?
I read the doc, but it's not specify. And I don't know how to test that.
nextflow
asked Nov 13 '18 at 22:02
Adam BellaïcheAdam Bellaïche
105
add a comment |
I have a process in Nextflow with multiple input file from a Channel.FromPath().
Here my script:
params.queries = ""
queries = Channel.fromPath(params.queries) #path to multiple .fasta files
process PsiBlast
input:
file query from queries_psiblast
output:
file top_hits
"""
blastpgp -d $db -i $query -j 2 -C ff.chd.ckp -Q pssm.out >> top_hits
"""
#then there are others processes, not needed for my question.
What I want to know is if my process is parallelized? If it run on 2 files at the same time for example? Or do I need to specify it in my script?
I read the doc, but it's not specify. And I don't know how to test that.
nextflow
asked Nov 13 '18 at 22:02
Adam BellaïcheAdam Bellaïche
105
add a comment |
I have a process in Nextflow with multiple input file from a Channel.FromPath().
Here my script:
params.queries = ""
queries = Channel.fromPath(params.queries) #path to multiple .fasta files
process PsiBlast
input:
file query from queries_psiblast
output:
file top_hits
"""
blastpgp -d $db -i $query -j 2 -C ff.chd.ckp -Q pssm.out >> top_hits
"""
#then there are others processes, not needed for my question.
What I want to know is if my process is parallelized? If it run on 2 files at the same time for example? Or do I need to specify it in my script?
I read the doc, but it's not specify. And I don't know how to test that.
nextflow
asked Nov 13 '18 at 22:02
Adam BellaïcheAdam Bellaïche
105
I have a process in Nextflow with multiple input file from a Channel.FromPath().
Here my script:
params.queries = ""
queries = Channel.fromPath(params.queries) #path to multiple .fasta files
process PsiBlast
input:
file query from queries_psiblast
output:
file top_hits
"""
blastpgp -d $db -i $query -j 2 -C ff.chd.ckp -Q pssm.out >> top_hits
"""
#then there are others processes, not needed for my question.
What I want to know is if my process is parallelized? If it run on 2 files at the same time for example? Or do I need to specify it in my script?
I read the doc, but it's not specify. And I don't know how to test that.
nextflow
nextflow
asked Nov 13 '18 at 22:02
Adam BellaïcheAdam Bellaïche
105
asked Nov 13 '18 at 22:02
Adam BellaïcheAdam Bellaïche
105
asked Nov 13 '18 at 22:02
Adam BellaïcheAdam Bellaïche
105
asked Nov 13 '18 at 22:02
Adam BellaïcheAdam Bellaïche
105
asked Nov 13 '18 at 22:02
Adam BellaïcheAdam Bellaïche
105
105
add a comment |
add a comment |
1 Answer
1
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Yes, Nextflow processes are implicitly parallelised provided there's are enough cpus/mem to fulfil the parallel execution.
answered Nov 14 '18 at 9:26
pditommasopditommaso
1,04021429
add a comment |
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1 Answer
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1 Answer
1
active
oldest
votes
active
oldest
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active
oldest
votes
Yes, Nextflow processes are implicitly parallelised provided there's are enough cpus/mem to fulfil the parallel execution.
answered Nov 14 '18 at 9:26
pditommasopditommaso
1,04021429
add a comment |
Yes, Nextflow processes are implicitly parallelised provided there's are enough cpus/mem to fulfil the parallel execution.
answered Nov 14 '18 at 9:26
pditommasopditommaso
1,04021429
add a comment |
Yes, Nextflow processes are implicitly parallelised provided there's are enough cpus/mem to fulfil the parallel execution.
answered Nov 14 '18 at 9:26
pditommasopditommaso
1,04021429
Yes, Nextflow processes are implicitly parallelised provided there's are enough cpus/mem to fulfil the parallel execution.
answered Nov 14 '18 at 9:26
pditommasopditommaso
1,04021429
answered Nov 14 '18 at 9:26
pditommasopditommaso
1,04021429
answered Nov 14 '18 at 9:26
pditommasopditommaso
1,04021429
answered Nov 14 '18 at 9:26
pditommasopditommaso
1,04021429
1,04021429
add a comment |
add a comment |
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