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feat: add consensus peaks subworkflow #37

Merged
merged 53 commits into from
Nov 29, 2023
Merged

feat: add consensus peaks subworkflow #37

merged 53 commits into from
Nov 29, 2023

Commits on Nov 21, 2023

  1. feat: add consensus peaks process [wip]

    @kelly-sovacool
    kelly-sovacool committed Nov 21, 2023
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Commits on Nov 22, 2023

  1. chore: Merge branch 'main' into consensus-peaks

    @kelly-sovacool
    kelly-sovacool committed Nov 22, 2023
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  2. fix: escape backslashes for nextflow template script

    @kelly-sovacool
    kelly-sovacool committed Nov 22, 2023
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  3. chore: Merge branch 'main' into consensus-peaks

    @kelly-sovacool
    kelly-sovacool committed Nov 22, 2023
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  4. fix: escape dollar signs for nf template

    @kelly-sovacool
    kelly-sovacool committed Nov 22, 2023
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  5. test: use macs2 peaks as test data

    @kelly-sovacool
    kelly-sovacool committed Nov 22, 2023
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  6. fix: metadata for consensuspeaks

    @kelly-sovacool
    kelly-sovacool committed Nov 22, 2023
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  7. test: add real md5sums for custom/consensuspeaks

    @kelly-sovacool
    kelly-sovacool committed Nov 22, 2023
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  8. fix: meta syntax

    @kelly-sovacool
    kelly-sovacool committed Nov 22, 2023
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  9. fix: write versions

    @kelly-sovacool
    kelly-sovacool committed Nov 22, 2023
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  10. chore: Merge branch 'main' into consensus-peaks

    @kelly-sovacool
    kelly-sovacool committed Nov 22, 2023
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  11. chore: Merge branch 'main' into consensus-peaks

    @kelly-sovacool
    kelly-sovacool committed Nov 22, 2023
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  12. feat: adapt bedtools modules from nf-core

    @kelly-sovacool
    kelly-sovacool committed Nov 22, 2023
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  13. refactor: minor cosmetic changes

    @kelly-sovacool
    kelly-sovacool committed Nov 22, 2023
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  14. chore: update changelog

    @kelly-sovacool
    kelly-sovacool committed Nov 22, 2023
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Commits on Nov 27, 2023

  1. fix: import platform

    @kelly-sovacool
    kelly-sovacool committed Nov 27, 2023
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  2. fix: switch nf-core -> ccbr

    @kelly-sovacool
    kelly-sovacool committed Nov 27, 2023
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  3. fix: use ccbr base docker

    @kelly-sovacool
    kelly-sovacool committed Nov 27, 2023
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  4. test: don't check md5sum of versions file

    @kelly-sovacool
    kelly-sovacool committed Nov 27, 2023
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  5. test: stub for custom/consensuspeaks module

    @kelly-sovacool
    kelly-sovacool committed Nov 27, 2023
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  6. docs: add bedtools modules

    @kelly-sovacool
    kelly-sovacool committed Nov 27, 2023
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  7. feat: add cat modules

    @kelly-sovacool
    kelly-sovacool committed Nov 27, 2023
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Commits on Nov 28, 2023

  1. feat: add bedops/bedmap module

    @kelly-sovacool
    kelly-sovacool committed Nov 28, 2023
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  2. style: align includes

    @kelly-sovacool
    kelly-sovacool committed Nov 28, 2023
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  3. test: add test for bedops/bedmap

    @kelly-sovacool
    kelly-sovacool committed Nov 28, 2023
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  4. feat: set default prefixes for bedtools processes 

    prevent the need to set task.ext.prefix in most cases
    @kelly-sovacool
    kelly-sovacool committed Nov 28, 2023
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  5. fix: propagate metadata correctly

    @kelly-sovacool
    kelly-sovacool committed Nov 28, 2023
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  6. chore: Merge branch 'main' into consensus-peaks

    @kelly-sovacool
    kelly-sovacool committed Nov 28, 2023
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  7. test: update test data config paths

    @kelly-sovacool
    kelly-sovacool committed Nov 28, 2023
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  8. refactor: fix ref bed name

    @kelly-sovacool
    kelly-sovacool committed Nov 28, 2023
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  9. refactor: don't delete intermediate files

    @kelly-sovacool
    kelly-sovacool committed Nov 28, 2023
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Commits on Nov 29, 2023

  1. feat: keep ref meta.id in bedmap outfiles

    @kelly-sovacool
    kelly-sovacool committed Nov 29, 2023
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  2. feat: create custom/combinepeaks module for consensus subwf

    @kelly-sovacool
    kelly-sovacool committed Nov 29, 2023
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  3. fix: template is nxf command, not bash

    @kelly-sovacool
    kelly-sovacool committed Nov 29, 2023
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  4. fix: define vars for Rscript template

    @kelly-sovacool
    kelly-sovacool committed Nov 29, 2023
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  5. feat: sort bed file to match original custom/consensuspeaks.py

    @kelly-sovacool
    kelly-sovacool committed Nov 29, 2023
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  6. test: create test yml for custom/combinepeaks

    @kelly-sovacool
    kelly-sovacool committed Nov 29, 2023
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  7. refactor: rename 'combinepeaks' -> 'combinepeakcounts'

    @kelly-sovacool
    kelly-sovacool committed Nov 29, 2023
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  8. feat: create module to normalize consensus peaks

    @kelly-sovacool
    kelly-sovacool committed Nov 29, 2023
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  9. refactor: set nxf variables as defaults

    @kelly-sovacool
    kelly-sovacool committed Nov 29, 2023
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  10. docs: update metadata for peak-related modules

    @kelly-sovacool
    kelly-sovacool committed Nov 29, 2023
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  11. docs: fix typo

    @kelly-sovacool
    kelly-sovacool committed Nov 29, 2023
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  12. feat: create consensus_peaks subwf 

    a replacement for the custom/consensuspeaks module
    @kelly-sovacool
    kelly-sovacool committed Nov 29, 2023
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  13. docs: add consensus_peaks subwf to changelog

    @kelly-sovacool
    kelly-sovacool committed Nov 29, 2023
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  14. docs: point users to consensus_peaks subwf from legacy module

    @kelly-sovacool
    kelly-sovacool committed Nov 29, 2023
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  15. chore: Merge branch 'main' into consensus-peaks

    @kelly-sovacool
    kelly-sovacool committed Nov 29, 2023
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  16. docs: move new modules & subwfs for next dev version

    @kelly-sovacool
    kelly-sovacool committed Nov 29, 2023
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  17. docs: license must be an array

    @kelly-sovacool
    kelly-sovacool committed Nov 29, 2023
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  18. test: creat test yml for consensus_peaks subwf

    @kelly-sovacool
    kelly-sovacool committed Nov 29, 2023
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  19. fix: typo in param name

    @kelly-sovacool
    kelly-sovacool committed Nov 29, 2023
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  20. test: add test for normalized & mixed consensus groups

    @kelly-sovacool
    kelly-sovacool committed Nov 29, 2023
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  21. fix: mix process versions channel

    @kelly-sovacool
    kelly-sovacool committed Nov 29, 2023
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  22. test: fix workflow entry name to mirrow new module name

    @kelly-sovacool
    kelly-sovacool committed Nov 29, 2023
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