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ground work for qc workflow #33

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merged 2 commits into from
Jul 9, 2022
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@Mxrcon Mxrcon commented Jul 1, 2022

Hey, as we discussed on our latest conversation, I started my partial work on the main qc workflow development trying to reach feature parity with h3agwas/qc.

I'd like to receive a review on this, we need to discuss the implementation paths into the internal logic of optional inputs need to be adapted to DSL-2 also the checked input is a channel manipulation technique that could be translated into a function or maybe a process to be executed. We can discuss the possibilities on this PR, I also decided to not touch the produceReports process until we shape the complete workflow methods.

I Kindly request your point of view on this small step onto the development on QC workflow, it certainly needs more organization and separation of the modules into sub-sub-workflows, but I'm not completely sure about this organization.

related to #32 and #29

Kindly, Davi.

@Mxrcon Mxrcon requested a review from abhi18av July 1, 2022 19:25
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@Mxrcon its looking good for the time being, just updated some references to file to path.

I'm merging it ahead to push my own changes soon.

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@abhi18av abhi18av merged commit 8549a54 into abhinav/qc-partial-2 Jul 9, 2022
abhi18av added a commit that referenced this pull request Aug 4, 2022
* manual formatting cleanup

* added a manifest for initial QC workflow

* ground work for qc workflow (#33)

* ground work for qc workflow

* Apply suggestions from code review [ci skip]

Co-authored-by: Abhinav Sharma <[email protected]>

* restructure modules within qc_* folders [ci skip]

* add remaining samplesheet process [ci skip]

* work on the local QC_WF [ci skip]

* add a qc_utils file to accommodate NF functions

* iteration on QC_WF design [ci skip]

* tweak flow from remove_duplicate_snps [ci skip]

* add the longer pathways in the subworkflow [ci skip]

* Annotate the right output channels [ci skip]

* simplify the flow to 3 key channels [ci skip]

* add the qc3_ch principal channel [ci skip]

* add another principal channel qc4 [ci skip]

* accomodate alternative pathways for find_rel_ch [ci skip]

* add config validation

* iterate on QC_VALIDATION

* iteration on input validation workflow

* initiate testing the input validation and other options

* add containers to config

* enable running only the qc subworkflow

* disable some validation checks to run pipeline

* fix module import issues

* test validation with allchro dataset

* validation workflow almost working

* disable the check for file exists on multimap

Co-authored-by: Davi Marcon <[email protected]>
@abhi18av abhi18av deleted the mxrcon/qc-partial-1 branch August 13, 2022 13:48
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2 participants