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feat: replace Python variables with pathvars - #46

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ahmig wants to merge 28 commits into

mainfrom

feat/pathvars

Open

feat: replace Python variables with pathvars#46
ahmig wants to merge 28 commits into
mainfrom
feat/pathvars

Commits on May 3, 2026
- replace output directory variable with pathvars
  ahmig
  committed
  e45863a
- replace logs directory variable with pathvars
  ahmig
  committed
  c752e29
- ci: update log packing
  ahmig
  committed
  660af2f
- replace report folder variables with pathvars
  ahmig
  committed
  a7ba5cc
- update .gitignore
  ahmig
  committed
  d79ff45
- revert CONTEXT_FASTA to null
  ahmig
  committed
  df8263e
- fix dataset pathvar in param
  ahmig
  committed
  7ed14e7
- remove support of Snakemake v7
  ahmig
  committed
  ba009a4
Commits on May 4, 2026
- ci: update logs folder
  ahmig
  committed
  c7e5376
Commits on May 6, 2026
- fix: use maximum precision for the time signal JSON
  ahmig
  committed
  ab4b025
Commits on May 17, 2026
- fix: ensure all key columns are present
  ahmig
  committed
  8ef5c15
Commits on Jun 4, 2026
- fix: fill missing dN and dS count categories with zero
  ahmig
  committed
  b697a7c
Commits on Jun 5, 2026
- fix missing column
  ahmig
  committed
  7b2831d
Commits on Jun 12, 2026
- fix: set max depth for mpileup
  ahmig
  committed
  6d7c81a
Commits on Jun 19, 2026
- fix: strip remove whitespace from parsed version
  ahmig
  committed
  8c2a218
Commits on Jun 30, 2026
- refactor: allow extra parameters on VCF fetch rule
  ahmig
  committed
  ed29627
- refactor: follow curl redirects for VCF by default
  ahmig
  committed
  17cd93f
Commits on Jul 8, 2026
- refactor: add amplitude and unique observation filters to pairwise correlations
  ahmig
  committed
  80f53ca
- refactor: update params names for clarity
  ahmig
  committed
  ec77665
Commits on Jul 17, 2026
- add param to combine pairwise correlation filter
  ahmig
  committed
  580588a
- update if-else pattern
  ahmig
  committed
  51f1b1b
- fix typo
  ahmig
  committed
  f870be4
Commits on Jul 22, 2026
- fail curl on HTTP errors
  ahmig
  committed
  8e58449
- update biopython environment
  ahmig
  committed
  c42e765
- fix escape sequences after pandas v3
  ahmig
  committed
  4b2b048
Commits on Aug 11, 2026
- fix: deduplicate alleles before afwdist run
  ahmig
  committed
  f71c04e
- fix: omit variants whose alternate allele matches the ancestor base
  ahmig
  committed
  4d53e5b
Commits on Sep 17, 2026
- refactor: coalesce rates to zero when no variants are present
  ahmig
  committed
  f24211a

Commits

Commits on May 3, 2026

Commits on May 4, 2026

Commits on May 6, 2026

Commits on May 17, 2026

Commits on Jun 4, 2026

Commits on Jun 5, 2026

Commits on Jun 12, 2026

Commits on Jun 19, 2026

Commits on Jun 30, 2026

Commits on Jul 8, 2026

Commits on Jul 17, 2026

Commits on Jul 22, 2026

Commits on Aug 11, 2026

Commits on Sep 17, 2026