Biohansel does not always correctly pair dataset collections in output

[DarianHole]

Not having an extension (ex .fastq) when making a collection of reads as an input for biohansel results in the final output not having the files paired even though the dataset collection does.

If I had to guess (and if I remember correctly) this is likely due to how the get_paired_fastq_filename function interacts with the $input.paired_collection.<forward|reverse> name which I believe utilizes the underlying name from the dataset used to make the collection and not the name in the collection itself

Example follows:

Dataset 1 -> Correctly pairs output:

• File names used to make up the paired collection:

  • TestX_R1.fastq && TestX_R2.fastq
  • TestY_R1.fastq && TestY_R2.fastq

• Paired Collection (looks the exact same as Dataset 2:
  

• Output:

TestX | heidelberg | 0.5.0

---

Dataset 2 -> Outputs are separated

• File names used to make up the paired collection:

  • TestX_R1 && TestX_R2
  • TestY_R1 && TestY_R2

• Paired Collection:
  

• Output:

TestX_R1 | heidelberg | 0.5.0
TestX_R2 | heidelberg | 0.5.0