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Update lib docs #5492
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#### The `lib` directory | ||||||||||||||||||||||||||||||
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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. | ||||||||||||||||||||||||||||||
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For example, `lib/DNASequence.groovy` defines the `DNASequence` class: | ||||||||||||||||||||||||||||||
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```groovy | ||||||||||||||||||||||||||||||
// lib/DNASequence.groovy | ||||||||||||||||||||||||||||||
class DNASequence { | ||||||||||||||||||||||||||||||
String sequence | ||||||||||||||||||||||||||||||
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// Constructor | ||||||||||||||||||||||||||||||
DNASequence(String sequence) { | ||||||||||||||||||||||||||||||
this.sequence = sequence.toUpperCase() // Ensure sequence is in uppercase for consistency | ||||||||||||||||||||||||||||||
} | ||||||||||||||||||||||||||||||
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// 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') | ||||||||||||||||||||||||||||||
int tCount = sequence.count('T') | ||||||||||||||||||||||||||||||
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// Wallace rule calculation | ||||||||||||||||||||||||||||||
double tm = 4 * (gCount + cCount) + 2 * (aCount + tCount) | ||||||||||||||||||||||||||||||
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Suggested change
@robsyme does this work for you? |
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return tm | ||||||||||||||||||||||||||||||
} | ||||||||||||||||||||||||||||||
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String toString() { | ||||||||||||||||||||||||||||||
return "DNA[$sequence]" | ||||||||||||||||||||||||||||||
} | ||||||||||||||||||||||||||||||
} | ||||||||||||||||||||||||||||||
``` | ||||||||||||||||||||||||||||||
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The `DNASequence` class is available in the execution context: | ||||||||||||||||||||||||||||||
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```nextflow | ||||||||||||||||||||||||||||||
// main.nf | ||||||||||||||||||||||||||||||
workflow { | ||||||||||||||||||||||||||||||
Channel.of('ACGTTGCAATGCCGTA', 'GCGTACGGTACGTTAC') | ||||||||||||||||||||||||||||||
.map { seq -> new DNASequence(seq) } | ||||||||||||||||||||||||||||||
.view { dna -> | ||||||||||||||||||||||||||||||
def meltTemp = dna.getMeltingTemperature() | ||||||||||||||||||||||||||||||
"Found sequence '$dna' with melting temperaure ${meltTemp}°C" | ||||||||||||||||||||||||||||||
} | ||||||||||||||||||||||||||||||
} | ||||||||||||||||||||||||||||||
``` | ||||||||||||||||||||||||||||||
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It returns: | ||||||||||||||||||||||||||||||
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``` | ||||||||||||||||||||||||||||||
Found sequence 'DNA[ACGTTGCAATGCCGTA]' with melting temperaure 48.0°C | ||||||||||||||||||||||||||||||
Found sequence 'DNA[GCGTACGGTACGTTAC]' with melting temperaure 50.0°C | ||||||||||||||||||||||||||||||
``` | ||||||||||||||||||||||||||||||
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### Data | ||||||||||||||||||||||||||||||
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but hard to read those variables maybe
g_count
orgc
is a better alternative