Groovy instanceof

Groovy example source code file (InstanceofTest.groovy)

Join Variable Numbers of Paths in Groovy

Cited from Joining Paths in Java

Paths#get(String first, String... more) states,

Converts a path string, or a sequence of strings that when joined form a path string, to a Path.

...

A Path representing an empty path is returned if first is the empty string and more does not contain any non-empty strings.

In Groovy, to print a variable number of arguments, the code is below.

import java.nio.file.*

String joinPath(String first, String... args){
Path path = Paths.get(first, args)
path.toString()
}

println joinPath('a')
println joinPath('a', 'b', 'c')
println joinPath('~/Data')

java.nio.file.Path Class in Groovy

Cited from Groovy Goodness: Extra Methods for NIO Path

Groovy adds a lot of extra methods to the File object to work with the contents or find and filter files in a directory. These methods are now also added to the java.nio.file.Path class since Groovy 2.3.

In a groovy script, the java.nio.file.Path class can be imported as the following. 

import java.nio.file.*

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Pass Varargs and Closure in Same Time to a Method?

How to pass varargs and closure in same time to a method?

Extract Sequences from Fasta

Cited from Toolkit for processing sequences in FASTA/Q formats

Extract sequences with names in file name.lst, one sequence name per line:

  seqtk subseq in.fq name.lst > out.fq

What is a Read Group?

Cited from Read Groups

There is no formal definition of what is a read group, but in practice, this term refers to a set of reads that were generated from a single run of a sequencing instrument.

In the simple case where a single library preparation derived from a single biological sample was run on a single lane of a flowcell, all the reads from that lane run belong to the same read group. When multiplexing is involved, then each subset of reads originating from a separate library run on that lane will constitute a separate read group.