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Diff bind reorg #45

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wants to merge 47 commits into from
Closed

Diff bind reorg #45

wants to merge 47 commits into from

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rroutsong
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refactoring and reorganization of the differential binding analyses

rroutsong added 18 commits August 15, 2024 18:14
@rroutsong
feat: add cftoolkit v0.6.0 w rmarkdown
4e0bdc9
@rroutsong
fix: inherit from docker v0.5.0
73f27db
@rroutsong
feat: move to static images for diff bind and uropa rules
8f402ec
@rroutsong
fix: rework diff bind and uropa scripts for modularity and new rules
368a33a
@rroutsong
fix: fix hooks, split diff bind and uropa into multiple rule hierarch…
08ad2fa 
…ical rules
@rroutsong
chore: remove planned new docker version
c1c7ff2
@rroutsong
fix: full path for config
bbf2310
@rroutsong
fix: set cwd at rule instead of script
d641467
@rroutsong
fix: cd to output dir in diff bind rule
0f78a9e
@rroutsong
fix: make sif cache aware of env
b77b72e
@rroutsong
fix: review changes
746452f
@rroutsong
fix: syntax error with rmarkdown::render
8ce07d2
@rroutsong
fix: images not image
9d200d7
@rroutsong
fix: remove references to container sif files
c16ac7b
@rroutsong
fix: pathing in rmarkdown and syntax in prep_diffbind
cacbd3a
@rroutsong
fix: split diffbind rules into multiple use cases
2063dbd
@rroutsong
fix: retool rule resources
f2d3e83
@rroutsong
chore: merge main
b9df531
tovahmarkowitz
tovahmarkowitz requested changes Sep 3, 2024
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skchronicles
skchronicles reviewed Sep 4, 2024
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Thank you for the updates! Let's wait on testing to finish before merging.

@rroutsong
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Sorry for the delay this is ready for review, data can be found at /data/OpenOmics/dev/datasets @tovahmarkowitz @skchronicles

@rroutsong rroutsong marked this pull request as draft September 17, 2024 15:12
@rroutsong rroutsong closed this Sep 17, 2024
rroutsong and others added 20 commits September 20, 2024 17:38
@rroutsong
fix: wildcard correction for expanded dba rules
20e3d35
@rroutsong
chore: resource allocation for dba rules update
d0bdfd0
@rroutsong
feat: validation of cfchip pipeline
e4b6c2a
@rroutsong
fix: uropa prep rule args
a3f9437
@rroutsong
feat: add uropa dockerfile
50c7b4a
@rroutsong
chore: add uropa update
61d4bd3
@rroutsong
fix: make new uropa container from bioconda
0e6b5fa
@rroutsong
fix: align inputs scripts and rules for diffbind and uropa functionality
8929e56
@rroutsong
Merge branch 'diff_bind_reorg' of http://github.com/OpenOmics/chrom-seek
ec5e985 
 into diff_bind_reorg
@rroutsong
feat: update resources on master job for local jobs
5fac49a
@rroutsong
fix: remove LANG def
353534b
@rroutsong
feat: new deduplication docker image
a9a2ab9
@rroutsong
fix: straighten out dedup dockerfile
94520db
@rroutsong
allow for uropa settings on cli instead of json key values
495f6aa
@rroutsong
linted
c97b396
@rroutsong
parameterize new jobs
b353112
@rroutsong
add new containers
d99e84a
@rroutsong
reconfigure how snakemake interacts with singularity
a334d43
@rroutsong
workflow changes for refactor of cfchip + diffbind + uropa sections
1afbf1d
@rroutsong
space
d190029
@rroutsong rroutsong reopened this Oct 24, 2024
@rroutsong rroutsong closed this Oct 24, 2024
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@tovahmarkowitz tovahmarkowitz tovahmarkowitz requested changes

@skchronicles skchronicles skchronicles left review comments

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@rroutsong @skchronicles @tovahmarkowitz @jlac