Code

Merge devel into main#252

Code

Merged

fasterius merged 172 commits intomainNBISweden/workshop-reproducible-research:mainfrom develNBISweden/workshop-reproducible-research:develCopy head branch name to clipboardNov 11, 2023

+33,961-25,324

Commits

Commits on May 5, 2023

• Add extra material on prettier Git logs

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Commits on Sep 7, 2023

• Change Nextflow installation instructions

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Commits on Sep 8, 2023

• Merge branch 'main' into devel

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• Update course id

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Commits on Sep 13, 2023

• Use multiqc instead of seqtk

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• Use bbmap instead of bowtie2

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Commits on Sep 14, 2023

• Merge pull request #245 from NBISweden/conda-basic-change

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• Change Rmarkdown to Quarto in overview figure

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• Change RMarkdown to Quarto on course overview page

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• Update location and application text

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• Add Lokesh as teacher

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• Add Quarto installation instructions

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• Add quarto-1-introduction page

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• Add section on course fee

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Commits on Sep 15, 2023

• Add TinyTex installation with Quarto

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• Add quarto-2-the-basics page

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• Add info on Quarto and LaTeX

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• Add section on Quarto Preview

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• Add note on naming Quarto code chunks

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• Add quarto-3-code-chunks page

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• Add quarto-4-document-options page

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Commits on Sep 18, 2023

• Change render to preview

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Commits on Sep 23, 2023

• Initial commit of snakemake quarto lecture

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Commits on Sep 24, 2023

• Add snakemake graphs

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• Explain snakemake mindset

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Commits on Sep 27, 2023

• Finish up snakemake quarto format lecture

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• Fix spelling

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• Add section on multiple Quarto output formats

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• Add page section on Quarto parameters

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• Use date: today Quarto option instead of R code

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• Add quarto-5-presentations page

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• Add material on chunk option param expressions

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• Add Quarto Conda environment

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• Add example of the final Quarto tutorial doc

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• Add quarto-6-extra-material page

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• Fix spelling and grammar throughout pages

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• Strip trailing whitespace throughout pages

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• Remove R Markdown material

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• Use dot language graphs instead of random image

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• Merge remote-tracking branch 'origin/quarto' into quarto

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• Update snakemake quarto lecture

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• Minor change to template

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Commits on Sep 28, 2023

• Clarify DAGs

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Commits on Sep 29, 2023

• Minor word change

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• Remove apostrophe

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Commits on Oct 4, 2023

• Remove R Markdown tutorial

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• Rename Quarto tutorial example file

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Commits on Oct 5, 2023

• Add jupyter lecture in quarto format

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• Merge branch 'quarto' of github.com:NBISweden/workshop-reproducible-research into quarto

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• Update jupyter lecture

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• Update gitignore

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• Add missing packages

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• Update snakemake lecture and remove unused files

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• Remove more unused files

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Commits on Oct 8, 2023

• Add conda quarto format lecture

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Commits on Oct 16, 2023

• Minor formatting

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• Add note to switch back to HTML rendering

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• Fix typo

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Commits on Oct 17, 2023

• Add text on using inline python

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• Add callout on jupyter engines

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• Reformat callout

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• Minor formatting change

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• Add point about removing inline python code

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• Clarify document options

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• Clarity overriding params from command line

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• Reformat code section

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Commits on Oct 18, 2023

• Update section on divs

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• Add papermill package to quarto env

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• Fix tabset

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• Make kernel selection more general

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Commits on Oct 20, 2023

• Add conda lecture in quarto format

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• Remove rmarkdown format lecture for conda

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• Replace conda pdf lecture with html

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• Add more info on callout titles

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• Update indentation

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• Update jupyter intro

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• Update jupyter dashboard image

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• Update empty notebook image

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Commits on Oct 21, 2023

• Update jupyter lecture

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• Update jupyter example image

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• Update jupyter basics page

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Commits on Oct 22, 2023

• Update .gitignore for Quarto

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• Update lecture Conda environment

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• Add Quarto project and NBIS extension

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• Change introduction lecture to Quarto; add images

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• Store lectures as HTML instead of PDF

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• Do not show links to other formats

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• Change layout and content in Conda lecture

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• Make only one, collected lecture Conda environment

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• Remove deprecated methods

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• Add more plotting packages

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Commits on Oct 23, 2023

• Update Conda lecture HTML

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• Convert container lecture to Quarto

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• Update data management lecture to Quarto

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• Convert Git lecture to Quarto

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• Convert Nextflow lecture to Quarto

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• Convert putting-it-together lecture to Quarto

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• Change image for jupyter widget

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• Move plotting libraries example

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• Update example on widgets for plotting

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Commits on Oct 24, 2023

• Update Snakemake lecture with NBIS template

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• Add reproducibility page for Jupyter module

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• Modify header

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• Update intro

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• Add text for using nbdime

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Commits on Oct 27, 2023

• Convert R Markdown lecture to Quarto

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• Update tool overview image with new logos

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• Change mentions of R Markdown to Quarto

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• Ignore Conda -env directories at lecture renders

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• Update lecture README.md

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• Do not use code line numbers in revealjs

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• Fix Conda/overview images

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• Add minor lecture fixes

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• Use NBIS template for Jupyter lecture

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• Remove the now unneeded Snakemake lecture pipeline

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• Remove unnecessary files from Git tutorial

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• Update lecture HTMLs

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Commits on Oct 28, 2023

• Change mention of Quarto creator Posit

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• Fix inconsistent naming of RStudio

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• Add rendered markdown example image

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• Change supplementary material to Quarto

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Commits on Oct 30, 2023

• Add note on Quarto revealjs bug

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Commits on Oct 31, 2023

• Add extra packages to jupyter-env

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• Add placeholder for papermill

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• Update section on reproducibility in jupyter

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Commits on Nov 2, 2023

• Merge branch 'quarto' into jupyter_update

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Commits on Nov 3, 2023

• Clarify that code-summary is a chunk option

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• Merge branch 'quarto' into jupyter_update

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• Minor formatting change

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• Add a callout on inline code and Quarto version

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• Minor formatting change

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• Add draft for new schedule

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• Add note on apt-get

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• Fix directory structure for Conda

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• Fix Snakemake directory structure

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• Fix Snakemake directory structure in pages

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• Fix container directory structure

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• Fix Jupyter directory structure

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• Fix mentions of intermediate/raw_<in/ex>ternal

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• Update DM lecture with new directory structure

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• Add small NBIS presentation to intro lecture

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• Move Git SSH setup to pre-course-setup

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Commits on Nov 4, 2023

• Remove text about deleting inline code

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• Merge branch 'quarto' of github.com:NBISweden/workshop-reproducible-research into quarto

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• Clarify code chunk options

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• Add full chunk option syntax

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• Add note on cap-location

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Commits on Nov 5, 2023

• Add text on setting code-summary in yaml header

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• Add note on supplying multiple params

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• Minor spelling and grammar corrections

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• Merge branch 'quarto' into jupyter_update

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Commits on Nov 6, 2023

• Update tutorial to be more in line with quarto

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Commits on Nov 7, 2023

• Merge branch 'devel' into quarto

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• Merge pull request #246 from NBISweden/quarto

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• Remove lecture render GitHub action

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• Fix broken link

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• Merge branch 'devel' into jupyter_update

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• Merge jupyter_update

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• Update schedule

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• Merge branch 'devel' into schedule

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• Clarify Quarto option loc; remove redundant note

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Commits on Nov 9, 2023

• Add course dinner to schedule

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Commits on Nov 11, 2023

• Merge pull request #248 from NBISweden/schedule

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• Merge branch 'devel' into structure

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• Merge pull request #249 from NBISweden/structure

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• Fix schedule formatting

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• Fix references to old files

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• Merge branch 'main' into devel

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• Fix GitHub actions with Quarto

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• Attempt to fix quarto/deno issue in GitHub actions

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• Separate Mamba install commands

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• Remove pinned deno/quarto versions for actions

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