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Resolve input from all tasks in join #35

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thejmazz opened this Issue Jul 11, 2016 · 3 comments

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thejmazz commented Jul 11, 2016

mpileupandcall needs the reference and bam, but as the per the join lineage:

const call = join(alignAndSort, samtoolsIndex, mpileupandcall)

it will only receive whichever samtoolsIndex provides as resolved output, which will just be the bai.
alignAndSort produces the bam, and receives the reference.

Current fix is to add

skipPassed: true

to the task so that it resolves input glob patterns from fs and not the output of the previous task.

So perhaps store all input and outputs of all tasks in a join lineage, and resolve inputs for tasks later on.

Nextflow does this by declaring "channels", pushing files into them, and pulling files out of them, explicitly, in separate tasks. Problem with that was need to manually duplicate channels to use the same file in other downstream tasks.

@thejmazz thejmazz referenced this issue Jul 11, 2016

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Timeline #2

16 of 38 tasks complete
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thejmazz commented Jul 11, 2016

  • some sort of state maintained (key, value) to access previously maintained files
  • needs to have some sort of uniqueness so that there are no overlaps
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thejmazz commented Jul 11, 2016

@yannickwurm

flexibility

  1. rna sras (ants, flies, etc.)
  2. filter
  3. transcriptome assembly (trinity -> trinity.fasta)
  4. pull out longest transcript
  5. take sra reads that contributed to assembly, map them to assembly (e.g. blast)
  6. fastq that only contains reads that contributed to this longest transcript

(Made it its own issue: #37)

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thejmazz commented Aug 17, 2016

uses DAG

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