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Update lib docs #5492

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53 changes: 52 additions & 1 deletion docs/sharing.md
Original file line number Diff line number Diff line change
Expand Up @@ -117,7 +117,58 @@

#### The `lib` directory

Any Groovy scripts or JAR files in the `lib` directory will be automatically loaded and made available to your pipeline scripts. The `lib` directory is a useful way to provide utility code or external libraries without cluttering the pipeline scripts.
The `lib` directory can be used to add utility code or external libraries without cluttering the pipeline scripts. The `lib` directory in the Nextflow project root is added to the classpath by default. Classes or packages defined in the `lib` directory will be available in the execution context. Scripts or functions defined outside of classes will not be available in the execution context.

For example, `lib/DNASequence.groovy` defines the `DNASequence` class:

```groovy
// lib/DNASequence.groovy
class DNASequence {
String sequence

// Constructor
DNASequence(String sequence) {
this.sequence = sequence.toUpperCase() // Ensure sequence is in uppercase for consistency
}

// Method to calculate melting temperature using the Wallace rule
double getMeltingTemperature() {
int gCount = sequence.count('G')
int cCount = sequence.count('C')
int aCount = sequence.count('A')

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but hard to read those variables maybe g_count or gc is a better alternative

int tCount = sequence.count('T')

// Wallace rule calculation
double tm = 4 * (gCount + cCount) + 2 * (aCount + tCount)

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Suggested change
int gCount = sequence.count('G')
int cCount = sequence.count('C')
int aCount = sequence.count('A')
int tCount = sequence.count('T')
// Wallace rule calculation
double tm = 4 * (gCount + cCount) + 2 * (aCount + tCount)
int g_count = sequence.count('G')
int c_count = sequence.count('C')
int a_count = sequence.count('A')
int t_count = sequence.count('T')
// Wallace rule calculation
double tm = 4 * (g_count + c_count) + 2 * (a_count + t_count)

@robsyme does this work for you?

return tm
}

String toString() {
return "DNA[$sequence]"
}
}
```

The `DNASequence` class is available in the execution context:

```nextflow
// main.nf
workflow {
Channel.of('ACGTTGCAATGCCGTA', 'GCGTACGGTACGTTAC')
.map { seq -> new DNASequence(seq) }
.view { dna ->
def meltTemp = dna.getMeltingTemperature()
"Found sequence '$dna' with melting temperaure ${meltTemp}°C"
}
}
```

It returns:

```
Found sequence 'DNA[ACGTTGCAATGCCGTA]' with melting temperaure 48.0°C
Found sequence 'DNA[GCGTACGGTACGTTAC]' with melting temperaure 50.0°C
```

### Data

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