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Brand wrappers #67

Merged
merged 116 commits into from
Feb 8, 2024
Merged

Brand wrappers #67

merged 116 commits into from
Feb 8, 2024

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cmeesters
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I am halfway pleased with the 'using wrapper' slides. The creation of wrappers is just too much at the moment: the reliance on Python knowledge is actually too heavy.

Do you agree @brand-fabian ? Eventually, it needs a bit of re-factoring and inclusion in yet another workshop?

@cmeesters
Getting_Started - no bug in PySam bioconda setup anymore, erased slid…
7f453f4 
…e mentioning this bug. Slides need further adaption. #12
@cmeesters
A_First_Workflow - fixed typo showing setup #12
26833fe
@cmeesters
added more workflow templates #12
9a34300
@cmeesters
moved cloze files to 'tutorial' for more convenient setup #12
842d2e5
@cmeesters
new differentiation in config.dat for cleaner setup #12
b9f46c3
@cmeesters
'tutorial' instead of 'cloze' for non-native speakers do not seem to …
c7f8d7e 
…know 'cloze' in config.dat for cleaner setup #12
@cmeesters
fixed typo in config.dat - needs reflection in files #12
767bd91
@cmeesters
add README file to describe the setup #12
7ac10f9
@cmeesters
changed preamble to reflect latest changes #12
4495f83
@cmeesters
renamed 'get_data.sh' to 'get_tutorial.sh' #12
ef6db90
@cmeesters
copy_script_template.sh - is added as template for the setup #12
9f6e8bb
@cmeesters
copy_script_template.sh - note about rsync and X11 forwarding has bee…
ec1a5c8 
…n added #12
@cmeesters
add 'copy_script_mogonII.sh' as an example, tested #12
0df1c7a
@cmeesters
creators/Sample_Data - coherent setup description #12
e9d3d59
@cmeesters
gnarf - non-change in material, just for testing
1d6492c
@cmeesters
reflecting latest changes on setup paths in 'common/condarc_mogon.tex' …
9b31664 
…#12
@cmeesters
added input/output wildcard cloze text and solution #12
53f5b3e
@cmeesters
creators/A_First_Workflow - additional slides to have a first trivial…
0dc8096 
… handout with cloze text #12
@cmeesters
report.html has accidentally been part of the repo #12
c88d7e3
@cmeesters
creators/A_First_Workflow - made the dummy rule a bit more 'sciency'
cf16a0d
@cmeesters
added mini task and solution for 'Further Decoration slide(s)
7a5a505
@cmeesters
config/config.dat - the pathtotutorial ought to be short in the slide…
fc87090 
…s, it is used after the copy step #12
@cmeesters
deleted conda stuff in 'workflows' directory. This is part of the set…
a1d0539 
…up now. #12
@cmeesters
added missing solution to solutions/02_Snakefile #12
b8baf67
@cmeesters
added solution and task to 03_Snakefile
b620893
@cmeesters
adaptions for 03 cloze text - not ready
b509659
@cmeesters
creators/A_First_Workflow - fixed typo breaking syntax #12
4a40634
@cmeesters
common/preamble - added minor explanation on HandsOn and Interlude in…
645ca5b 
…structions #12
@cmeesters
creators/A_First_Workflow - forgotten work commit - added mini hands …
28d6179 
…on for wildcards, causes merge conflict #12
@cmeesters
creators/A_First_Workflow - resolved merge conflict
a353bbc
@cmeesters cmeesters mentioned this pull request Feb 4, 2024
Closed
cmeesters and others added 16 commits February 4, 2024 14:52
@cmeesters
Merge pull request #52 from cmeesters/sample_files_#12
a669179 
Updated Sample files  #12
feat: Adding slides explaining the setup, usage and creation of snake…
f934787 
…make wrappers.

This is a first attempt to provide some slides to explain all aspects
of wrappers in some depth.

Refs: #44
@cmeesters
common/wrapper - inserted optical frame separators
e57baf5
@cmeesters
moved common/wrapper.tex -> common/using_wrappers.tex
d1e30fc
@cmeesters
Snakemake_HPC_Creators - reflecting name change
bca2bd2
@cmeesters
adapted sections and disentagled tex files for wrappers
c7907c2
@cmeesters
common/using_wrappers - introduced consistent usage of the Snakemake …
9e5258e 
…layout
@cmeesters
adapt_sections.py - will silently ignore configured tex files
137d01e
@cmeesters
common/using_wrappers - changed wrapper doc URL to readthedocs-link
e4db978
@cmeesters
common/using_wrappers - re-arragned and corrected layout - better did…
692abdf 
…actics?
@cmeesters
Snakemake_HPC_Creators - including using and coding wrappers
84b670b
@cmeesters
creators/coding_wrappers - added frame separators
911da90
@cmeesters
Snakemake_HPC_Creators.tex - outcommented the creation of wrappers - …
6cf45b7 
…too much for this course
fix: Changed files paths in Snakemake_HPC_Users.tex to existing files.
e00f418
fix: adding include hook that fails when a file is missing.
6287891
fix: Preparing to merge wrappers into main.
a73e1e1 
Merge branch 'brand-wrappers' of https://github.com/cmeesters/snakemake-hpc-teaching-material into brand-wrappers

Refs: #67, #44
@brand-fabian
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@cmeesters Thanks for your help in getting the slides up to the required standard. I have updated the PR by updating the base commit (somehow github seems to now include all commits from main here, idk why 😅 ) and making sure it builds against the current Snakemake_HPC_Users.tex file.

I have made some changes:

  1. I added an include hook in preamble.tex to make sure that the CI works as expected, i.e. it will now fail if an included file is missing. Previously, since latexmk returns 0 for such errors, it would still show the green checkmark despite an actual build failure.
  2. Changed Snakemake_HPC_Users.tex to include the correct using_wrappers tex file.

@cmeesters
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cool! As I have been the one doing the PR - will you want to review (and merge)?

@brand-fabian brand-fabian merged commit f51ea04 into main Feb 8, 2024
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@cmeesters cmeesters deleted the brand-wrappers branch February 8, 2024 14:28
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