Nextflow : Is it possible to tranform a queue channel to a value channel?
I have a process A which outputs a file into a channel outA. I want to use that file as input for 3 downstream processes B, C and D. As the channel outA created is a queue channel by default, I cannot directly use the file more than once (unlike value channels).
Currently, I use the into operator to duplicate the channel outA as described here (see the code below).
I also know that you can create a value channel from a file by doing Channel.value(file('/path/to/file.txt')).
My code currently :
// Upstream process creating a queue channel with one file
process A {
output:
file outA
"echo 'Bonjour le monde !' > $outA"
}
// Queue channel triplication
outA.into {inB; inC; inD}
// Downstream processes all using the same file
process B {
input:
file inB
"script of process B $inB"
}
process C {
input:
file inC
"script of process C $inC"
}
process D {
input:
file inD
"script of process D $inD"
}
I works fine as it is, but I wonder if it is possible to transform the queue channel outA into a value channel, so that I can use the same channel as input for processes B, C and D.
nextflow
asked Dec 29 '18 at 18:34
JetJet
53
add a comment |
I have a process A which outputs a file into a channel outA. I want to use that file as input for 3 downstream processes B, C and D. As the channel outA created is a queue channel by default, I cannot directly use the file more than once (unlike value channels).
Currently, I use the into operator to duplicate the channel outA as described here (see the code below).
I also know that you can create a value channel from a file by doing Channel.value(file('/path/to/file.txt')).
My code currently :
// Upstream process creating a queue channel with one file
process A {
output:
file outA
"echo 'Bonjour le monde !' > $outA"
}
// Queue channel triplication
outA.into {inB; inC; inD}
// Downstream processes all using the same file
process B {
input:
file inB
"script of process B $inB"
}
process C {
input:
file inC
"script of process C $inC"
}
process D {
input:
file inD
"script of process D $inD"
}
I works fine as it is, but I wonder if it is possible to transform the queue channel outA into a value channel, so that I can use the same channel as input for processes B, C and D.
nextflow
asked Dec 29 '18 at 18:34
JetJet
53
add a comment |
I have a process A which outputs a file into a channel outA. I want to use that file as input for 3 downstream processes B, C and D. As the channel outA created is a queue channel by default, I cannot directly use the file more than once (unlike value channels).
Currently, I use the into operator to duplicate the channel outA as described here (see the code below).
I also know that you can create a value channel from a file by doing Channel.value(file('/path/to/file.txt')).
My code currently :
// Upstream process creating a queue channel with one file
process A {
output:
file outA
"echo 'Bonjour le monde !' > $outA"
}
// Queue channel triplication
outA.into {inB; inC; inD}
// Downstream processes all using the same file
process B {
input:
file inB
"script of process B $inB"
}
process C {
input:
file inC
"script of process C $inC"
}
process D {
input:
file inD
"script of process D $inD"
}
I works fine as it is, but I wonder if it is possible to transform the queue channel outA into a value channel, so that I can use the same channel as input for processes B, C and D.
nextflow
asked Dec 29 '18 at 18:34
JetJet
53
I have a process A which outputs a file into a channel outA. I want to use that file as input for 3 downstream processes B, C and D. As the channel outA created is a queue channel by default, I cannot directly use the file more than once (unlike value channels).
Currently, I use the into operator to duplicate the channel outA as described here (see the code below).
I also know that you can create a value channel from a file by doing Channel.value(file('/path/to/file.txt')).
My code currently :
// Upstream process creating a queue channel with one file
process A {
output:
file outA
"echo 'Bonjour le monde !' > $outA"
}
// Queue channel triplication
outA.into {inB; inC; inD}
// Downstream processes all using the same file
process B {
input:
file inB
"script of process B $inB"
}
process C {
input:
file inC
"script of process C $inC"
}
process D {
input:
file inD
"script of process D $inD"
}
I works fine as it is, but I wonder if it is possible to transform the queue channel outA into a value channel, so that I can use the same channel as input for processes B, C and D.
nextflow
nextflow
asked Dec 29 '18 at 18:34
JetJet
53
asked Dec 29 '18 at 18:34
JetJet
53
edited Dec 29 '18 at 21:20
Jet
asked Dec 29 '18 at 18:34
JetJet
53
asked Dec 29 '18 at 18:34
JetJet
53
asked Dec 29 '18 at 18:34
JetJet
53
53
add a comment |
add a comment |
1 Answer
1
active
oldest
votes
You can use the first() operator to do that, e.g.:
inX = outA.first()
process B {
input:
file inX
"script of process B $inX"
}
etc
Also note that when a process has no input (like process A) its outputs are implicitly value channels.
answered Jan 2 at 9:20
pditommasopditommaso
1,04021429
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
You can use the first() operator to do that, e.g.:
inX = outA.first()
process B {
input:
file inX
"script of process B $inX"
}
etc
Also note that when a process has no input (like process A) its outputs are implicitly value channels.
answered Jan 2 at 9:20
pditommasopditommaso
1,04021429
add a comment |
You can use the first() operator to do that, e.g.:
inX = outA.first()
process B {
input:
file inX
"script of process B $inX"
}
etc
Also note that when a process has no input (like process A) its outputs are implicitly value channels.
answered Jan 2 at 9:20
pditommasopditommaso
1,04021429
add a comment |
You can use the first() operator to do that, e.g.:
inX = outA.first()
process B {
input:
file inX
"script of process B $inX"
}
etc
Also note that when a process has no input (like process A) its outputs are implicitly value channels.
answered Jan 2 at 9:20
pditommasopditommaso
1,04021429
You can use the first() operator to do that, e.g.:
inX = outA.first()
process B {
input:
file inX
"script of process B $inX"
}
etc
Also note that when a process has no input (like process A) its outputs are implicitly value channels.
answered Jan 2 at 9:20
pditommasopditommaso
1,04021429
answered Jan 2 at 9:20
pditommasopditommaso
1,04021429
answered Jan 2 at 9:20
pditommasopditommaso
1,04021429
answered Jan 2 at 9:20
pditommasopditommaso
1,04021429
1,04021429
add a comment |
add a comment |
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