Make a list file (outputs.list) from the output of previous task.

Dear all,
I wrote a WDL script which generates multiple g.vcf files from my different samples (inspired by your WDL scripts) using HaplotypeCallerERC. I need to make the output of my previous task to be into one file (outputs.list) to pass it as an argument in the next tool which will be CombineGVCFs. IS that possible? And what is your suggestion for that please?
Thanks in advance
Nawar

Best Answer

  • edited November 14 Accepted Answer

    I assume you are using ascatter to generate the g.vcf files. In that case, you can see an example in this workflow:
    the output of the first task PairedFastQsToUnmappedBAM is collected by the second task CreateFoFN into an Array[String] which is than used to create a text file with one filename (string) per line. Check also the write_lines function.

    Hope this helps

    p.s. Hi Nawar, I'm Dario from the Sevilla Workshop, how are you?

    Post edited by dario_romagnoli on

Answers

  • dario_romagnolidario_romagnoli Member
    edited November 14 Accepted Answer

    I assume you are using ascatter to generate the g.vcf files. In that case, you can see an example in this workflow:
    the output of the first task PairedFastQsToUnmappedBAM is collected by the second task CreateFoFN into an Array[String] which is than used to create a text file with one filename (string) per line. Check also the write_lines function.

    Hope this helps

    p.s. Hi Nawar, I'm Dario from the Sevilla Workshop, how are you?

    Post edited by dario_romagnoli on
  • Thank you very much Dario for this wonderful help. It is exactly what I was looking for.
    I am fine by the way, thanks for asking. Hope to hear from you again soon.
    Take care

Sign In or Register to comment.