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Update optional-input.nf #50

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79b54d4
Update optional-input.nf
cmatKhan May 19, 2025
878fdea
Update optional-input.md
cmatKhan May 19, 2025
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16 changes: 6 additions & 10 deletions docs/optional-input.md
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Original file line number Diff line number Diff line change
Expand Up @@ -4,35 +4,31 @@ One or more processes have an optional input file.

## Solution

Use a special file name to mark the absence of the file parameter.

Create an empty file in `assets`:
```
touch assets/NO_FILE
```
Pass an empty array to the optional input. The empty array will be evaluated to `false`.

## Code

```groovy
params.inputs = "$projectDir/data/prots/*{1,2,3}.fa"
params.filter = "$projectDir/assets/NO_FILE"
// pass a empty array. this evaluates to false
params.filter = []

process foo {
debug true
debug true
input:
path seq
path opt

script:
def filter = opt.name != 'NO_FILE' ? "--filter $opt" : ''
def filter = opt ? "--filter ${opt}" : ""
"""
echo your_command --input $seq $filter
"""
}

workflow {
prots_ch = Channel.fromPath(params.inputs, checkIfExists:true)
opt_file = file(params.filter, checkIfExists:true)
opt_file = file(params.filter)

foo(prots_ch, opt_file)
}
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5 changes: 3 additions & 2 deletions optional-input.nf
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Expand Up @@ -27,7 +27,8 @@
*/

params.inputs = "$projectDir/data/prots/*{1,2,3}.fa"
params.filter = "$projectDir/assets/NO_FILE"
// pass a empty array. this evaluates to false
params.filter = []

process foo {
debug true
Expand All @@ -36,7 +37,7 @@ process foo {
path opt

script:
def filter = opt.name != 'NO_FILE' ? "--filter $opt" : ''
def filter = opt ? "--filter ${opt}" : ""
"""
echo your_command --input $seq $filter
"""
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