Code

add command-line level validations#159

Code

Merged

pdimens merged 27 commits intomainpdimens/harpy:mainfrom cli_validationspdimens/harpy:cli_validationsCopy head branch name to clipboardNov 5, 2024

+537-266

Commits

Commits on Oct 31, 2024

• add harpytype

  pdimens

  committed
  a7c4f16

Commits on Nov 1, 2024

• improve genome input

  pdimens

  committed
  00a5ddf

• fix fasta checks for new logic

  pdimens

  committed
  7b6d367

• rm validate by ext

  pdimens

  committed
  a2af4ee

• add snakemake validation

  pdimens

  committed
  fe2cf0b

• swap to conda

  pdimens

  committed
  ed39b0d

• add HPC cli type and validation

  pdimens

  committed
  75a046d

• rename to generic to add program-specific file

  pdimens

  committed
  1bd9370

• add fastp param validation

  pdimens

  committed
  e492be3

• add frag density as an option

  pdimens

  committed
  964365d

• add extra params validations

  pdimens

  committed
  ba807e4

• realistic example

  pdimens

  committed
  e2f3a93

• add spades param clu

  pdimens

  committed
  d159fb3

• add Arcs param validation

  pdimens

  committed
  493dfaa

• simplify the cli and with a dict

  pdimens

  committed
  996e24b

• add stitch param validation

  pdimens

  committed
  49f1712

• clarify text

  pdimens

  committed
  910cdfa

• add hapcut extra validatio

  pdimens

  committed
  055f618

• stage snp params validations

  pdimens

  committed
  313991c

• add urls

  pdimens

  committed
  ad035c7

Commits on Nov 4, 2024

• add snp params

  pdimens

  committed
  07500c0

• fixes

  pdimens

  committed
  1ff9d39

• add contigs/scaff to quast and give better label names

  pdimens

  committed
  9212929

• add new cli file to filters

  pdimens

  committed
  7314c4d

• touch up printing

  pdimens

  committed
  c8d46b9

• improve logic such that the message only appears if the plugin isn't in the environment already

  pdimens

  committed
  36cd006

• nicer formatting

  pdimens

  committed
  408114b