8000 Update to DSL2 and add in Transcript Identification by edmundmiller · Pull Request #24 · nf-core/nascent · GitHub
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Update to DSL2 and add in Transcript Identification #24

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Merged
merged 624 commits into from
Mar 16, 2022
Merged

Update to DSL2 and add in Transcript Identification #24

merged 624 commits into from
Mar 16, 2022

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edmundmiller
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@edmundmiller edmundmiller commented Sep 30, 2021 •
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From Slack:

I've committed a bit of a party foul. Last March (2020) I started converting our labs pipeline that I had originally written in snakemake to follow the nf-core standard because I was coming up with similar stuff for our snakemake pipelines and would rather work with a larger community. We'd like to add it to nf-core. Anyways, I missed the part about reaching out on slack to see if there's an duplicate work. It's a groseq pipeline, which the #nascent pipeline covers but we're using a couple of different methods.
I started on DSL2 pre-template when @hpatel first converting rnaseq. I've got it updated to the latest template last week. I would like to wrap into nascent, I'm just not sure if they're doing the same thing. Ours uses either homer in a workflow our lab created in a previous paper using Homer, or following another one called TFSEE that @venkat Malladi's group came up with that uses grohmm. #nascent seems to be just creating the bedGraphs and bigwigs
I just see that as a 3 possible pathway after you've got the reads aligned and all. homer, grohmm, or just producing graphs from the reads.
I'm not sure whether the homer/grohmm can cover proseq or cageseq etc.
What I propose doing git repowise, I think ours has more relevant history and then I can reimplement the nascent stuff if it's worth it in DSL2 really easily. We can archive the #nascent pipeline since there's been no active development on it, and then we'll give acknowledgements to the archived repo. I'd love to get others thoughts.

This should be a rebase merge, since I already took care of the big merge locally.

If we decide to merge this, things that need to be done:

sruthips 10000 uresh and others added 30 commits February 10, 2021 11:34
@sruthipsuresh @edmundmiller
Removed input files which weren't used
acaafbf
@edmundmiller
test(grohmm): Fix test command
427a352
@edmundmiller
test(grohmm): Restructure for more consistent testing
376befb
@edmundmiller
test(grohmm): Use github data
90a9ead 
Can't test offline, so no working on grohmm on a flight.
@edmundmiller
test(grohmm): Rewrite to test each module individually
e2aec97
@edmundmiller
fix(grohmm): Take a tuple instead just a path
69d37bf
@sruthipsuresh @edmundmiller
Added options for strand
919dca0
@sruthipsuresh @edmundmiller
Add tuning parameters in csv file, test csv file
722a026
@sruthipsuresh @edmundmiller
TODO test ganymede
fb5cc04
@sruthipsuresh @edmundmiller
Fixed parameter tuning seq len
1249b00
@edmundmiller
Fixed bed output issue
ace5dc6
@edmundmiller
ci: Add local modules tests for pytest-workflow
36b708c
@edmundmiller
test: Fix config profiles
f9ee7b7
@edmundmiller
test(grohmm): Remove profiles
7059fe4
@edmundmiller
ci: Use self-hosted runner for now
d265e8b
@edmundmiller
ci: Skip nextflow install step
570d080
@edmundmiller
feat(prepare_genome): Add gffread options
ac91932
@edmundmiller
feat(prepare_genome): Add subworkflow call
cfed8fa
@edmundmiller
fix(prepare_genome): Add all the other references
94e48ca
@edmundmiller
chore: Add boilerplate options
b8f31e6
@edmundmiller
fix(prepare_genome): Use new module
498afad
@edmundmiller
chore: Bump nextflow required version
b4ebd24 
Cause plugins
@edmundmiller
fix(prepare_genome): Add filter_gtf_for_genes_in_genome
e45913d
@edmundmiller
Merge remote-tracking branch 'glue' into develop
6f42025
@edmundmiller
feat(bwa): Add initial run through
f87dcbf
@edmundmiller
fix(bwa): The index is getting untar'd in prepare_genome
1f08fad
@edmundmiller
style: Fix order of imports
cbb000a
@edmundmiller
Fixed map issue that was undetected by nextflow run
13fac08
@nithyaj12 @edmundmiller
added remove genes modules to do testing
f40d43e
@sruthipsuresh @edmundmiller
Added test for module, TODO sloprefseq, TODO switch to subworkflow
028adce
@edmundmiller
feat(dreg): Initialize module
22df195
@edmundmiller
fix(dreg): Update to peakcalling
afe2075 
Since the docker image uses an old version of dREG it still has
"peakcalling" as the script.
Danko-Lab/dREG@b3038b8
@edmundmiller
feat(coverage): Add bedgraphtobigwig
3cbfd41 
IDK if this works because it's broken on my local cluster
@edmundmiller
fix(homer): Set as default transcript identification
14431cc
@edmundmiller
fix(homer): Add strand separate
8ee113d 
Gotta keep 'em seperated.
Hey!
@edmundmiller
fix(homer): Change output file of makeucscfile
7b89a0c 
This prevents changing the tag_dir, which should fix caching of
findPeaks and makeucscfile.
@edmundmiller
style(homer): Update out path
205e5b1
@edmundmiller edmundmiller changed the title Merge in Groseq Update to DSL2 and add in Transcript Identification Feb 28, 2022
@edmundmiller
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To be clear, this is just merging into dev. Still need to write some tests and what not, but I'd like to break those into smaller PRs

@edmundmiller edmundmiller requested review from ignaciot and magruca March 1, 2022 16:56
@edmundmiller edmundmiller self-assigned this Mar 3, 2022
@edmundmiller edmundmiller added this to the V2 milestone Mar 3, 2022
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ignaciot commented Mar 8, 2022

Hi Edmund,

Life has become increasingly busier since I first put out the nascent pipeline, and I'm having a hard time finding the time to update it after every template change. So, your plan sounds fine to me if you decide to merge this with your GRO-seq pipeline.

@drpatelh
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Will merge this in for now in favour of reviewing this properly before the release.

drpatelh
drpatelh approved these changes Mar 16, 2022
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🚀

@drpatelh drpatelh merged commit 92fc710 into dev Mar 16, 2022
@edmundmiller edmundmiller deleted the groseq branch March 16, 2022 15:35
This was referenced Mar 16, 2022
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@drpatelh drpatelh drpatelh approved these changes

@vsmalladi vsmalladi Awaiting requested review from vsmalladi

@ignaciot ignaciot Awaiting requested review from ignaciot

@magruca magruca Awaiting requested review from magruca

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