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Feature/add main drug res workflow#39

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kathrynmurie wants to merge 77 commits intodevfrom
feature/add_main_drug_res_workflow
Draft

Feature/add main drug res workflow#39
kathrynmurie wants to merge 77 commits intodevfrom
feature/add_main_drug_res_workflow

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@kathrynmurie kathrynmurie commented Aug 29, 2025 •
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This PR inlcudes the full pipeline linking the modules together

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • Make sure your code lints (nf-core pipelines lint).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

kathrynmurie and others added 30 commits January 21, 2025 18:46
@kathrynmurie
Create basic workflow to allele prev
ab8267b
@kathrynmurie
Merge branch 'dev' into feature/add_main_drug_res_workflow
4778d90
@kathrynmurie
add coi to workflow
77047d6
@kathrynmurie
Add multilocus method
2f994c0
@kathrynmurie
Add MLAF workflow
40095d8
@kathrynmurie
Add param validation workflow
0128be2
@kathrynmurie
Add more input validation
4d881d5
@kathrynmurie
Merge branch 'dev' into feature/add_main_drug_res_workflow
124fcbd
@kathrynmurie
Outline reference method
918dd6e
@kathrynmurie
Add help message
96b4101
@kathrynmurie
Begin moving workflow to nf-core template
c8cf553
@kathrynmurie
Merge in dev changes
250e1f7
@kathrynmurie
Add subworkflows
6d68ab5
@kathrynmurie
Add working workflow to nf-core template
18ae317
@kathrynmurie
Create inputs in pipeline initialisation workflow
9f17290
@kathrynmurie
Add back in option to supply allele table with bed file
f14d135
@kathrynmurie
remove outputs
5053aab
@kathrynmurie
Remove old workflow. Update PGEcore. Add more tools to workflow
82f268d
@kathrynmurie
Create final output tables
0a2638d
@kathrynmurie
Remove running COI in main workflow as output is unused currently
ed3338e
@kathrynmurie
Add input schema. Removed checks on schema for now. Update PGEcore
31792f5
@kathrynmurie
Update MLBM with output path; Add FEM as option
0f7d46a
@kathrynmurie
Add per population functionality
c88e43d
@kathrynmurie
Add option to run with single population and set label
a991a96
@kathrynmurie
Update tests
8d0dff2
@kathrynmurie
Tidy plasmodiumdrugres workflow
8abe1b0
@nickjhathaway
added FEM to Dockerfile; set R version to 4.4* within Dockerfile;
82a8388
@kathrynmurie
remove some template files
e81a1bb
@kathrynmurie
Update schema, params, and validation. Removed validation for allele …
0f760f7 
…table
@kathrynmurie
Ensure resources are set for each module
dc06566
kathrynmurie and others added 15 commits September 2, 2025 21:27
@kathrynmurie
Update hash for fem test
3bac491
@kathrynmurie
Match MLBM test md5sum to when docker build without silicon chip
e5ee618
@kathrynmurie
Add pop column to mlaf output
b40e1c0
@nickjhathaway
updated PMO example for newer format; update modules extract_allele_t…
0b45d0d 
…able for argument changes to pmotools-python;
@nickjhathaway
Merge branch 'feature/add_main_drug_res_workflow' of github.com:Plasm…
117bdfe 
…oGenEpi/plasmodiumdrugres into feature/add_main_drug_res_workflow

* 'feature/add_main_drug_res_workflow' of github.com:PlasmoGenEpi/plasmodiumdrugres:
  Add pop column to mlaf output
@nickjhathaway
update md5sum;
d4258f8
@nickjhathaway
linting;
83e3942
@nickjhathaway
fix for relative paths for main workflow;
6cd6de7
@nickjhathaway
add naive method as a possible algorithm for multilocus;
336476f
@nickjhathaway
exposed a new MLBM argument for filtering low occurrence aa calls;
6db23f6
@nickjhathaway
Merge pull request #42 from PlasmoGenEpi/hotfix/allow_passing_of_MLBM…
1e73858 
…_cut_off_value

exposed a new MLBM argument for filtering low occurrence aa calls;
@nickjhathaway
added naive multilocus estimator; updated outputs to include more inf…
88b5244 
…ormation about what was submitted;
@nickjhathaway
updated the new dcifer wrapper name;
2a8fc2e
@nickjhathaway
various small tweaks to update unit tests to make things work; added …
e11081d 
…more example files for unit tests;
@nickjhathaway
Added modules and scripts to do single locus allele frequency from mi…
f04cbcf 
…crohaplotype frequencies; updated tests and MD5 sums to reflect changes in PGEcore scripts output; updated multillocus naive to include method;
@nickjhathaway nickjhathaway marked this pull request as draft February 26, 2026 22:33
kathrynmurie and others added 14 commits March 9, 2026 15:13
@kathrynmurie
Merge pull request #44 from PlasmoGenEpi/feature/adding_slaf_from_mha…
d071c6a 
…p_af

Updating main drug resistance pipeline
@kathrynmurie
extract mhap_freq method as option in slaf subworkflow
5ebda09
@kathrynmurie
Update PGEcore to dev branch; remove unused input params
d7e20a8
@kathrynmurie
fix schema v config conflicts; update docs; Add all params to schema
c563a52
@kathrynmurie
Fix pre-commit check
31f111e
@kathrynmurie
fix bug in split_table_by_population_map.R
10ad8eb
@kathrynmurie
resolve some linting issues
953a3cb
@kathrynmurie
add contributors to config
6417190
@kathrynmurie
Template update for nf-core/tools version 3.5.2
7d571ad
@kathrynmurie
Merge branch 'TEMPLATE' into feature/add_main_drug_res_workflow
1cbf846
@kathrynmurie
add linting changes
4239b66
@kathrynmurie
Fix linting
8524a9b
@kathrynmurie
Add input param back in as a hidden input option to make linting test…
b50dd16 
…s pass
@kathrynmurie
Add citations, contributors, handle some linting warnings
c4fb55c
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2 participants

@kathrynmurie @nickjhathaway