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Update from the development fork#42

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zachary-foster wants to merge 236 commits intonf-core:masternf-core/pathogensurveillance:masterfrom grunwaldlab:mastergrunwaldlab/pathogensurveillance:masterCopy head branch name to clipboard

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Commits

Commits on Sep 13, 2023

• ensured all outputs are named by IDs and made output names more clear

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• added SNP alignment to test input data for main report

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Commits on Sep 14, 2023

• fixed a few channel operations breaking the cache

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• added depth-based read subsetting to speed up variant calling

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• changed report from bookdown to quarto

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Commits on Sep 15, 2023

• test

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• minor

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• random changes testing things

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• merge

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• remove python

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• added summary formatting

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• minor

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• date format changed

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• date format

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• fixed table format

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• minor

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• changed to having all libaries loaded in a chunk at top for the rest of the document.

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Commits on Sep 17, 2023

• minor edits

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• added draft about stuff. maybe this could be moved to one palced and linked several times throughout

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Commits on Sep 18, 2023

• added stats for # samples

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• submitter names parsed

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• minor edits

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• minor changes

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Commits on Sep 19, 2023

• changes to about

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• added contributor

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• added parameters to control subsampling

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• Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

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• various changes including methods section and first citations

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• minor edit

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Commits on Sep 20, 2023

• Just testing before making a few updates

  

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• change to biblio ref

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• fix to subsampling code

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

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• typo

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

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• Adding comments and playing with MSN and SNP tree options

  

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• Updates to SNP tree

  

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• more test data inputs, but qmds still need updates

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

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• ANI matrix explorations

  

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• updates-snp tree

  

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

  

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• quick updates to diversity report

  

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Commits on Sep 21, 2023

• added parsing of new inputs

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• merge

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• updates to diversity.qmd

  

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

  

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• Quick updates to continue testing MSN functions

  

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• Made report mostly work with new test data and pipeline

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• merge

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• Early work on diversity.qmd-very rough!

  

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• Quick updates to organization of diversity doc.

  

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• Quick fixes to headers as I figure out organization

  

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Commits on Sep 24, 2023

• Updates to diversity.qmd

  

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Commits on Sep 25, 2023

• minor

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• tried to embed softre_Versions.yml file with all versions. should probably be embeded as text rather than links.

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• include statement reads software_versions.yml, but does not break lines correctly.

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• deleted embed

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• software versions used are now displayed.

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Commits on Sep 26, 2023

• Quick updates to render .qmd file

  

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• update

  

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Commits on Sep 28, 2023

• adding sketch table and still playing with it.

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• Sendsketch table draft done - Camilo

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• make report output as a single HTML file

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• added custom css

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• changed static table to interactive

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• removed top nav bar, added CSS

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

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Commits on Sep 29, 2023

• quick updates to diversity section

  

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• minor theme changes

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• merge

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• fixed some errors when using non-test data

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Commits on Oct 2, 2023

• Added requirement for report group

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• Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

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• made input to main report just the run directory

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• made new test data that is easier to switch between

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Commits on Oct 3, 2023

• created a favicon, but it is not displaying where I want to.

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• updates

  

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

  

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• updates

  

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• Updates

  

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• make reports all go into the same output directory

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• fix software versions not being tracked for much of the pipeline

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

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• fix bug due to no taxa being found in sendsketch results

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• adding while loop to improve reference picking

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Commits on Oct 4, 2023

• SNP tree revisions

  

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• SNP tree update

  

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• Revising how sample names parsed for SNP analyses

  

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• fixed divide by zero error when attempting to subsample low-depth samples

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

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• Merge branch 'master' into dev

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• revise tip labels and strain names-Snp analysis

  

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

  

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• SNP analysis update

  

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• added a footer with osu and usda logos.

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• added fotoer and logos

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• minor edits

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

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• Minor edits to headers

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• moved about seciton to end

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• added nf-core logo

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• minor edits

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• more detials added to footer

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• typo

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• minor edit

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• ANI tree

  

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

  

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Commits on Oct 5, 2023

• started work on handling errors/warnings and passing them to the report

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

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• ggtree plotly updates

  

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

  

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• added icon collection and some icon images

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• added icons

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• more icons

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• added acknowledgement for icon libraries.

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• change to feedback item

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• icon added

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• added R logo

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• minor edit

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• added nf-core reference

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Commits on Oct 6, 2023

• undo testing change

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

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• more work on trying to get status updates to the main report

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Commits on Oct 10, 2023

• updates

  

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

  

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• minor

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

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• fixes versiondump bug

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• redid main report inputs to allow for missing inputs from skipped processes

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Commits on Oct 11, 2023

• treechart to report % of samples clasified as X taxa - needs more work.

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• comments from Nik

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Commits on Oct 12, 2023

• disable circos plotting in bakta that sometimes causes errors

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Commits on Oct 13, 2023

• removed unneeded nesting in main workflow to make progress printing better (breaks cache)

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• Stop optional columns with commas causing incorrect CSV parsing

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• display the whole taxonomy with plotly using the sunburst and treemap plot types

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Commits on Oct 14, 2023

• update

  

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

  

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Commits on Oct 16, 2023

• Updates to NJ tree

  

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• images

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• icon libraries

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

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Commits on Oct 17, 2023

• added 'color_by' column to example data

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

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• Adding a few notes

  

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• Ensure that reference IDs are assigned to a single unique reference path. resolves nf-core#23

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

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• Notes for diversity section

  

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Commits on Oct 20, 2023

• Updates to ANI outputs

  

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• test graphics from dash-plotly-python and observable JS

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

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• tree updates

  

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

  

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• small edits

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• new

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

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• example plotly ggrtree with reference to url

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Commits on Oct 23, 2023

• Updates to ANI tree

  

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• Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance into dev

  

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• tree output updates

  

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• Tree updates

  

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• Make more informative labels for tree and ANI matrix

  

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Commits on Oct 24, 2023

• MSN updates

  

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Commits on Oct 25, 2023

• Updates poppr portion

  

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• Testing different MSN outputs

  

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Commits on Oct 31, 2023

• Quick changes MSN

  

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Commits on Nov 2, 2023

• trying to fix duplicated logo on readme

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• clean up report and move images to their own directory

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• merge

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Commits on Nov 9, 2023

• Bib update

  

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• Updates

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