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feat: differential binding analysis with diffbind or manorm #158

Merged
merged 41 commits into from
Dec 18, 2023
Merged

feat: differential binding analysis with diffbind or manorm #158

merged 41 commits into from
Dec 18, 2023

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kelly-sovacool
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@kelly-sovacool kelly-sovacool commented Nov 28, 2023 •
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Changes

  • Optionally read in contrasts yaml file.
    • can contain multiple contrasts.
    • each contrast specifies two groups, with an exclusive list of samples for each group.
  • If the contrasts file is specified, do differential peak analysis
    • Run MAnorm if any sample has only one replicate, or diffbind if all samples have at least two replicates.

Issues

PR Checklist

(Strikethrough any points that are not applicable.)

  • This comment contains a description of changes with justifications, with any relevant issues linked.
  • [ ] Write unit tests for any new features, bug fixes, or other code changes. testing framework not yet implemented
  • [ ] Update docs if there are any API changes. on hold until before public release
  • If a new nextflow process is implemented, define the process container and stub.
  • Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

@kelly-sovacool
feat: add Rmd for diffbind from legacy pipeliner
c48fc3b 
source: https://github.com/CCBR/Pipeliner/blob/86c6ccaa3d58381a0ffd696bbf9c047e4f991f9e/Results-template/Scripts/DiffBind_pipeliner.Rmd
@kelly-sovacool
test: add columns for diff groups
ecf0116
@kelly-sovacool
feat: create module to check contrasts & write modified samplesheet
fe0010f
@kelly-sovacool
chore: Merge branch 'samplesheet-groups' into diffbind
adec520
@kelly-sovacool
chore: Merge branch 'main' into diffbind
c515201
@kelly-sovacool
fix: call check_contrasts in main.nf
88e2412
@kelly-sovacool
fix: use validated csv, include contrast in output
fa61c9d
@kelly-sovacool
feat: emit validated csv
aa2327d
@kelly-sovacool
feat: create diff subworkflow
aa11706 
combine peaks with contrast meta
@kelly-sovacool
fix: also need bam files for diffbind
d53ac8d
@kelly-sovacool
feat: create module to prepare sample sheet for diffbind
6332e0b
@kelly-sovacool
feat: enforce contrast & tool must be the same
dbd32c5
@kelly-sovacool
fix: include ctrl bam/bai for diffbind [wip]
f09db39
@kelly-sovacool
fix: use collectFile to avoid filename collisions in prep_diffbind
bb9c77b
@kelly-sovacool
feat: install nf-core/rmarkdownnotebook process
9a9d696
@kelly-sovacool
fix: error in collectFile
c8c384a 
nextflow-io/nextflow#4559
@kelly-sovacool
feat: render diffbind report
54a5f99
@kelly-sovacool
refactor: move diffbind rmd to assets/
11429ab
@kelly-sovacool
refactor: improve channel operations for diffbind rmd
b9b441a
@kelly-sovacool
feat: check that each sample only appears in one group
30673c9
@kelly-sovacool
chore: Merge branch 'diffbind' of https://github.com/CCBR/CHAMPAGNE i…
234bbd6 
…nto diffbind
@kelly-sovacool
feat: patch rmarkdownnotebook w/ custom container & stub
39b2cf9
@kelly-sovacool
refactor: set meta.id
2f28edc
@kelly-sovacool
fix: set rmarkdown parameters in same channel as files
79e910e
@kelly-sovacool
fix: csv concatentation w/ newlines
bbf8bb2
@kelly-sovacool
fix: add new line to end of converted sicer bed files
34c480b
@kelly-sovacool
fix: don't fail to plot peak widths when gem is only peak caller
1f173ef
@kelly-sovacool
refactor: switch example contrast names
6c39c6b
@kelly-sovacool
chore: Merge branch 'diffbind' of https://github.com/CCBR/CHAMPAGNE i…
78fc8d2 
…nto diffbind
@kelly-sovacool
refactor: remove EdgeR diffbind analysis
4f93d34
@kelly-sovacool kelly-sovacool changed the title feat: differential binding analysis with diffbind feat: differential binding analysis with diffbind or manorm Dec 14, 2023
@kelly-sovacool kelly-sovacool marked this pull request as ready for review December 18, 2023 21:06
@kelly-sovacool kelly-sovacool merged commit 7735706 into main Dec 18, 2023
2 checks passed
@kelly-sovacool kelly-sovacool deleted the diffbind branch December 18, 2023 21:12
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Successfully merging this pull request may close these issues.

Refactor samplesheet check for flexibility Differential peak calling
1 participant
@kelly-sovacool