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Overhaul of myco_sra #48

Merged
merged 15 commits into from
Mar 21, 2024
Merged

Overhaul of myco_sra #48

merged 15 commits into from
Mar 21, 2024

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aofarrel
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@aofarrel aofarrel commented Mar 19, 2024 •
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Overhauls myco_sra to be more like myco_raw.

  • Combine fastp with the decontamination step
  • Implement fastq-TBProfiler
    • bam-TBProfiler is still there, but is now mutually exclusive with fastq-TBProfiler
  • Rip out fastQC
  • Add process for collating QC information, although since this workflow usually runs multi-sample, this isn't as important as it is for myco_raw
  • Simplify the workflow process overall
  • Heavily reduce the number of workflow-level inputs
  • Update documentation

@aofarrel
Update prereqs, remove fastQC
f410682
@aofarrel
Big overhaul
9237bd0 
With the exception of TBProf_on_bams_not_fastqs and the pull task, this is now very close to how myco_raw works
@aofarrel
TBProfiler stuff now possible tree annotation
b81a157
@aofarrel
Don't subsample twice
64575a7
@aofarrel
Fix always fail coverage QC, rm error reporting, fix runtime(ish) typ…
13ef574 
…e error, JSONs

The type error doesn't show up in miniwdl check, but when you go to run it fails immediately. Curious! Or different versions of miniwdl? After all, it is being checked locally but run on SB...
@aofarrel
Cleanup, update docs
5b779ce
@aofarrel
Update link
62adf93
@aofarrel
Update myco_sra.wdl
33409e8
@aofarrel
Update myco_sra.wdl
ec99918
@aofarrel
Test older version of covstats
008a6cb
@aofarrel
Test older version of covstats
1239401
@aofarrel
Merge branch 'better-myco_sra' of https://github.com/aofarrel/myco in…
67afa49 
…to better-myco_sra
@aofarrel
Update TBProfiler
74982d7
@aofarrel
Leverage TSVs properly
b2cf0c2
@aofarrel
Revert testing change
d6b29bc
@aofarrel aofarrel merged commit 1017447 into main Mar 21, 2024
1 check passed
@aofarrel aofarrel deleted the better-myco_sra branch March 21, 2024 05:18
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@aofarrel