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Optional task ? e.g: merge sam files in number of fastqs > 1

What's the correct way to execute an optional task ?
For example if my input looks like

samples: [
  { name : "Sample1", fastqs : [ ["S1.001.R1.fastq","S1.001.R2.fastq"] ,["S1.002.R1.fastq","S1.002.R2.fastq"]] },
  { name : "Sample2", fastqs : [ ["S2.001.R1.fastq","S2.001.R2.fastq"] ] },

for Sample1 I would merge S1.001.bam and S1.002.bam while it's not required for Sample2


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