clip_adapters: false


- condition1: embryo
  condition2: larva
  metadata: phenotype



- SAMN00990702-1
- SAMN00990702-2
- SAMN00990702-3
- SAMN00990703-1
- SAMN00990703-2
- SAMN00990703-3

- files:

    bam: pipeline/SAMN00990702-1/mappings/accepted_hits.bam

name: SAMN00990702-1

output_folder: pipeline/SAMN00990702-1
- files:

    bam: pipeline/SAMN00990702-2/mappings/accepted_hits.bam

name: SAMN00990702-2

output_folder: pipeline/SAMN00990702-2

- files:
    bam: pipeline/SAMN00990702-3/mappings/accepted_hits.bam
    name: SAMN00990702-3
  output_folder: pipeline/SAMN00990702-3
- files:
    bam: pipeline/SAMN00990703-1/mappings/accepted_hits.bam
    name: SAMN00990703-1
  output_folder: pipeline/SAMN00990703-1
- files:
    bam: pipeline/SAMN00990703-2/mappings/accepted_hits.bam
    name: SAMN00990703-2
  output_folder: pipeline/SAMN00990703-2
- files:
    bam: pipeline/SAMN00990703-3/mappings/accepted_hits.bam
    name: SAMN00990703-3
  output_folder: pipeline/SAMN00990703-3]

  How can I give a command which initially read the comparisons and it takes that to [metadata][phenotype][embryo] and which takes that to samples -> files ->bam which is the input

This question is difficult to understand. I don't think the wall of output text helps. Maybe you could word it differently, or provide a little pseudo-code to help us understand what exactly you are trying to do?

What are the comparisons? A file?

What does "takes that to [metadata][phenotype][embryo]" mean? (what does "takes that to" mean in python?)

"samples -> files -> bam which is the input"..input to what?

A lot have people have viewed your question, but I think the wording is making it hard to help.

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