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feat: Add gene order subworkflow #131

Merged
merged 34 commits into from
Nov 12, 2023
Merged

feat: Add gene order subworkflow #131

merged 34 commits into from
Nov 12, 2023

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jvfe
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@jvfe jvfe commented Jun 15, 2023

jvfe added 18 commits June 15, 2023 11:09
@jvfe
feat: Use all possible combinations for alignment
21d434c
@jvfe
Try fixing clustering
ffaab75
@jvfe
fix: Add upstream fixes from Julia
b530610
@jvfe
feat: Add gene order modules to output dir
b7903a5
@jvfe
fix: Emit correct outputs in clustering.nf
d402e03
@jvfe
refactor: Make extraction output have _temp suffix
b7622f8
@jvfe
refactor: Change visualization.py to use plotly CDN
8574c97
@jvfe
feat: Add --plot_clustering to optionally make HTML files
f538e5a
@jvfe
chore: Add Gene Order params to schema
f2b6e82
@jvfe
refactor: Remove original temp JSON file from output
f5c2040
@jvfe
Merge branch 'master' into gene-order-workflow
4b7accc 
* master:
  fix: Change create_report back to high_memory
  refactor: Use collect output in filter/add_column and optional report (#139)
  refactor: Increase default reqs for ppanggolin and create_report (#137)
  feat: Check sample ID validity with Annotation input check (#136)
  feat: Add annotation tools param (#134)
  docs: Add new ARETE logo (#135)
  feat: Add param to skip the pan/phylo subwf (#132)
@jvfe
chore: Add Julia's changes from the latest update
9a66d1c
@jvfe
feat: Add gene order subwf to ARETE
922e6d4
@jvfe
refactor: Swap containers to docker ones
9d8a93f
@jvfe
refactor: Update singularity image
5382f39
@jvfe
Revert "refactor: Update singularity image"
9f0d3ff 
This reverts commit 5382f39.
@jvfe
refactor: Change skip to run
b1ec4a5
@jvfe
fix: Change indenting
725edfd
@jvfe jvfe marked this pull request as ready for review June 29, 2023 12:59
@jvfe
feat: Add changes from cba3ca4 and 9a5a9a
73ee729
@jvfe
style: Add black to other bin/ files
8a3a40f
@jvfe
refactor: Remove gene order HTML template from code
b5fdfd7
@jvfe
Merge branch 'master' into gene-order-workflow
bc0cd3c 
* master:
  feat: Add recombination entry (#175)
  docs: Add evolCCM usage documentation
  feat: Add evolCCM entry (#174)
  docs: Update rSPR outputs (#173)
  fix: Stop ppanggolin msa from altering input file (#172)
  feat: Add rspr entry (#171)
  refactor: Ignore time reached error in rspr_exact (#170)
@jvfe
fix: Remove mentions of html-template
46496c6
@jvfe
docs: Add gene order to output and params
000bc97
@jvfe jvfe merged commit 6b7e268 into master Nov 12, 2023
4 checks passed
@jvfe jvfe deleted the gene-order-workflow branch November 12, 2023 14:00
jvfe added a commit that referenced this pull request Nov 12, 2023
@jvfe
Merge branch 'master' into poppunk-viz-skip
73271bd 
* master:
  feat: Add gene order subworkflow (#131)
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Incorporate gene order workflow into ARETE
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@jvfe