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ngstk API agreement, chipseq as guinea pig for pypiper.Pipeline and checkpoint framework #8

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ngstk API agreement, chipseq as guinea pig for pypiper.Pipeline and checkpoint framework #8

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vreuter
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@vreuter vreuter commented Oct 25, 2017 •
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Some now-unused code lingers in chipseq.py, but I think it should remain until the newer version get some more in-the-wild testing.
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vreuter added 30 commits August 14, 2017 17:10
@vreuter
Sample set_file_paths signature
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@vreuter
signature changes in ATAC also
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@vreuter
access library value via attribute rather than key so that deprecatio…
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…n doesn't cause problem; invert conditional logic to ease comprehension
@vreuter
generalizing the tools and resources paths
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reflect dependency of each pipeline on pypiper and of most on looper
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@vreuter
access protocol/library info via Sample API not from raw input data
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catch when ip mark is not identified in the annotations and simplify …
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…the handling of broad/histone flag setting
@vreuter
case homogenization within the marks
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@vreuter
assign bigwig path
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provide path to script
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allow for non-CeMM filepaths
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@vreuter
point to available SPP
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@vreuter
type socket cluster
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@vreuter
name the worker nodes for cluster creation
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@vreuter
cast cores count to int
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revert to drop-in value once spp is available
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use the peak quality toolkit environment variable
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@vreuter
make pipeline reflect pypiper dev branch ngstk function parameter names
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try matching keys to as in ATAC
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spelling for grep
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use stat dict accessor
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merged changes from master to fix the lack of a model during plot att…
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…empt
@vreuter
account for empty/NA ways to designate control sample/s
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place sample's bigwig file in its output folder, not in a bigwig fold…
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…er in project output folder
@vreuter
statistical significance specification flexibility
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first pass at pulling out common arguments in peak callers and specif…
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…ying signficance value
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clarify plotting workflow
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share the model filenames suffix
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use the broad mark indicators from the config file
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@vreuter
remove itertools import
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@afrendeiro
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Hey @vreuter this is shaping up very nicely!
I think pypiper.Pipeline is also quite a good idea.
I just had a general look but recently haven't had much time to follow closely. Will you let me know when things are at a point to review/test?

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vreuter commented Nov 6, 2017

Thanks! Yep, will do.

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vreuter commented Nov 19, 2017

Hey @afrendeiro I think whenever you're ready, this is set for review. Retained still is the original code for comparison in case anything breaks, but that can be removed once this has been used a bit more frequently/heavily and confidence increases. It's been working well in the last few runs, though, so it can be reviewed now.

@afrendeiro afrendeiro force-pushed the dev branch 2 times, most recently from 1298114 to e1c6f66 Compare April 3, 2018 14:51
@nsheff nsheff requested a review from afrendeiro November 6, 2018 15:31
@afrendeiro afrendeiro closed this Feb 28, 2019
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