Add qc workflow - Githubissues

msk-access / access_qc_generation

Generation Quality Controls Files for MSK-ACCESS

https://cmo-ci.gitbook.io/access-quality-control-v2/

Apache License 2.0

1 stars 1 forks source link

Add qc workflow #6

Closed murphycj2 closed 3 years ago

ionox0 commented 3 years ago

It would be cleaner to use record types instead of parallel lists, for example:

type: record
fields:
  sample_id: string
  sample_type: string
  sample_sex: string
  simplex_bam: File
  duplex_bam: File
  collapsed_bam: File
  uncollapsed_bam: File
  ...

Then we can scatter over a single array of sample records, as opposed to many separate lists

Perhaps we can refactor this

murphycj2 commented 3 years ago

@ionox0 not sure what record types would look like. I am just using what rabix outputs by default. feel free to refactor though

ionox0 commented 3 years ago

I've got almost all steps running but have a few things left

[x] I need to add the general_stats_parse.py step to the main workflow
[x] I need https://github.com/msk-access/cwl-commandlinetools/pull/107 merged to fix sequence_qc filenames (hopefully this will still be compatible with our multiQC config)
[ ] documentation

Hopefully these things will be all that's left as far as I'm aware @rhshah @murphycj2

ionox0 commented 3 years ago

todo:

[ ] make sure outputs are structured ok
[ ] include version number in all cwl-commandlinetool step names
[ ] test on multiple samples
[ ]