How to indicate to nextlow where takes output?
up vote
0
down vote
favorite
I have a script in python which save a file in a specific directory.
For example this code named "write.py":
with open("project/results/txt/output.txt", "w") as f:
f.write("this is a txt file")
So I execute my script in "project/src" and the output of this script is in "project/results/txt/".
Here an example of a script Nextflow in "project/":
process writeTxt{
output:
file "output.txt"
"""
python3 ../../../src/write.py
"""
}
"../../../" ==> to go out of work directory
But nextflow return that it didn't find "projet/results/txt/output.txt".
So how indicates to Nextflow where is the output of a script?
nextflow
asked Nov 21 at 16:33
Adam Bellaïche
105
add a comment |
up vote
0
down vote
favorite
I have a script in python which save a file in a specific directory.
For example this code named "write.py":
with open("project/results/txt/output.txt", "w") as f:
f.write("this is a txt file")
So I execute my script in "project/src" and the output of this script is in "project/results/txt/".
Here an example of a script Nextflow in "project/":
process writeTxt{
output:
file "output.txt"
"""
python3 ../../../src/write.py
"""
}
"../../../" ==> to go out of work directory
But nextflow return that it didn't find "projet/results/txt/output.txt".
So how indicates to Nextflow where is the output of a script?
nextflow
asked Nov 21 at 16:33
Adam Bellaïche
105
add a comment |
up vote
0
down vote
favorite
up vote
0
down vote
favorite
I have a script in python which save a file in a specific directory.
For example this code named "write.py":
with open("project/results/txt/output.txt", "w") as f:
f.write("this is a txt file")
So I execute my script in "project/src" and the output of this script is in "project/results/txt/".
Here an example of a script Nextflow in "project/":
process writeTxt{
output:
file "output.txt"
"""
python3 ../../../src/write.py
"""
}
"../../../" ==> to go out of work directory
But nextflow return that it didn't find "projet/results/txt/output.txt".
So how indicates to Nextflow where is the output of a script?
nextflow
asked Nov 21 at 16:33
Adam Bellaïche
105
I have a script in python which save a file in a specific directory.
For example this code named "write.py":
with open("project/results/txt/output.txt", "w") as f:
f.write("this is a txt file")
So I execute my script in "project/src" and the output of this script is in "project/results/txt/".
Here an example of a script Nextflow in "project/":
process writeTxt{
output:
file "output.txt"
"""
python3 ../../../src/write.py
"""
}
"../../../" ==> to go out of work directory
But nextflow return that it didn't find "projet/results/txt/output.txt".
So how indicates to Nextflow where is the output of a script?
nextflow
nextflow
asked Nov 21 at 16:33
Adam Bellaïche
105
asked Nov 21 at 16:33
Adam Bellaïche
105
asked Nov 21 at 16:33
Adam Bellaïche
105
asked Nov 21 at 16:33
Adam Bellaïche
105
asked Nov 21 at 16:33
Adam Bellaïche
105
105
add a comment |
add a comment |
1 Answer
1
active
oldest
votes
up vote
0
down vote
accepted
This is an anti-pattern. Nextflow tasks are expected to produce and consume files in task execution directory. If such output file is produced by a upstream task, that must be declared as task output to make it accessible in the task work directory.
answered Nov 21 at 16:56
pditommaso
1,01021429
How Can I declare this? I don't know the way to do that.
– Adam Bellaïche
Nov 21 at 17:12
because I started Nextflow last week.
– Adam Bellaïche
Nov 22 at 8:21
add a comment |
1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
up vote
0
down vote
accepted
This is an anti-pattern. Nextflow tasks are expected to produce and consume files in task execution directory. If such output file is produced by a upstream task, that must be declared as task output to make it accessible in the task work directory.
answered Nov 21 at 16:56
pditommaso
1,01021429
How Can I declare this? I don't know the way to do that.
– Adam Bellaïche
Nov 21 at 17:12
because I started Nextflow last week.
– Adam Bellaïche
Nov 22 at 8:21
add a comment |
up vote
0
down vote
accepted
This is an anti-pattern. Nextflow tasks are expected to produce and consume files in task execution directory. If such output file is produced by a upstream task, that must be declared as task output to make it accessible in the task work directory.
answered Nov 21 at 16:56
pditommaso
1,01021429
How Can I declare this? I don't know the way to do that.
– Adam Bellaïche
Nov 21 at 17:12
because I started Nextflow last week.
– Adam Bellaïche
Nov 22 at 8:21
add a comment |
up vote
0
down vote
accepted
up vote
0
down vote
accepted
This is an anti-pattern. Nextflow tasks are expected to produce and consume files in task execution directory. If such output file is produced by a upstream task, that must be declared as task output to make it accessible in the task work directory.
answered Nov 21 at 16:56
pditommaso
1,01021429
This is an anti-pattern. Nextflow tasks are expected to produce and consume files in task execution directory. If such output file is produced by a upstream task, that must be declared as task output to make it accessible in the task work directory.
answered Nov 21 at 16:56
pditommaso
1,01021429
answered Nov 21 at 16:56
pditommaso
1,01021429
answered Nov 21 at 16:56
pditommaso
1,01021429
answered Nov 21 at 16:56
pditommaso
1,01021429
1,01021429
How Can I declare this? I don't know the way to do that.
– Adam Bellaïche
Nov 21 at 17:12
because I started Nextflow last week.
– Adam Bellaïche
Nov 22 at 8:21
add a comment |
How Can I declare this? I don't know the way to do that.
– Adam Bellaïche
Nov 21 at 17:12
because I started Nextflow last week.
– Adam Bellaïche
Nov 22 at 8:21
How Can I declare this? I don't know the way to do that.
– Adam Bellaïche
Nov 21 at 17:12
How Can I declare this? I don't know the way to do that.
– Adam Bellaïche
Nov 21 at 17:12
because I started Nextflow last week.
– Adam Bellaïche
Nov 22 at 8:21
because I started Nextflow last week.
– Adam Bellaïche
Nov 22 at 8:21
add a comment |
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