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Pulling back rubicon into master #118

Merged
merged 38 commits into from
Jan 6, 2022
Merged

Pulling back rubicon into master #118

merged 38 commits into from
Jan 6, 2022

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DrYak
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@DrYak DrYak commented Jan 6, 2022

Features:

  • CI/CD: Megalinter, kill old jobs
  • visualisation: phylogeny and alignement
  • new smallgenomeutiliteies 0.3.5 (frameshift_deletions_checks)
  • handle malformed samples TSV

External utils:

  • mass-importers
  • fixes in installer (follow; messages)

Documentation:

  • utils
  • sync config (new diversity section)
  • preliminary jupytext in docs

kpj and others added 30 commits January 6, 2022 16:16
@kpj @DrYak
Add MegaLinter GA workflow
3ca4b3c
@kpj @DrYak
Set default branch to master
c7591f0
@kpj @DrYak
Make sure to validate whole codebase
6bf8e3c
@kpj @DrYak
Update to megalinter@v5
a5d3d2f
@kpj @DrYak
Fix shellcheck issues
0163619
@kpj @DrYak
Fix markdownlint issues
452f8bb
@kpj @DrYak
[Mega-Linter] Apply linters fixes
4afc0c3
@kpj @DrYak
Revert "[Mega-Linter] Apply linters fixes"
3e955c6 
This reverts commit e8ad826.
@kpj @DrYak
Explicitly disable applying MegaLinter fixes
784b602
@kpj @DrYak
Disable flavor suggestions
4c15581
@kpj @DrYak
Add MegaLinter badge
149832f
@kpj @DrYak
[Mega-Linter] Apply linters fixes
bfce55e
@kpj @DrYak
Revert "[Mega-Linter] Apply linters fixes"
b690b53 
This reverts commit 0c42c2a.
@kpj @DrYak
Try another way of disabling automatic MegaLinter fixes
33ec388
@kpj @DrYak
[Mega-Linter] Apply linters fixes
7cb5a72
@kpj @DrYak
Revert "[Mega-Linter] Apply linters fixes"
1409b0c 
This reverts commit 4caaf56.
@kpj @DrYak
This time disabling will surely work
4ed4a0f
@kpj @DrYak
Black formatting
3d258cb
@kpj @DrYak
Fix disabled asterisk expansion
c07b0d8
@kpj @DrYak
Fix LICENSE.md recognition by GitHub
bac757f
@kpj @DrYak
Improve error handling of cd commands
23ca006
@kpj @DrYak
Fix shellcheck's SC2015
74aac1e
@DrYak
More explicit crash message on badly formated TSV (+snakefmt shenigans)
d810ce7 
 - Explicitely point out the TSV error
 - TODO samples_schema.json
 - (Also snakefmt changed a few other things. For... reasons?)
@kpj @DrYak
GA workflow resource conservation
7a189d0 
* Make GA workflows cancel previous unfinished runs for new commits on the same branch
@kpj @DrYak
Make README.md introduction clearer
7b85845
@kpj @DrYak
Move previous job cancelling to own section
93faa8a
@DrYak
add phylogeny and read alignment
b112603
@DrYak
fix if statement in visualization.smk
162ff76
@kpj @DrYak
Add shebang to docs/convert.sh
bbd5017
@kpj @DrYak
Fix shellcheck's SC2035
f3839c4
kpj and others added 8 commits January 6, 2022 16:18
@kpj @DrYak
Disable MD040 where we don't need it
c139206
@kpj @DrYak
Snakefmt formatting
7df3f4d
@kpj @DrYak
Bad fix for MD040
3297d2a
@DrYak
Installer fixes
aeb9de8 
 - fix #114 
   - switcher to newer URL with `refs/tags/`
   - `curl -L`: follow redirects
 -  Clearer failure messages
@DrYak
Upgrade smallgenomeutilites
6ba6a43 
 - new frameshift_deletions_checks
@DrYak
Samples mass-importers utils
81314ea 
 - importer for loose files
 - importers with info from dmx
 - documentation for all utils
   (+quick_install)
@DrYak @LaraFuhrmann
Proof reading typo fixes
7dbdd82 
Co-authored-by: LaraFuhrmann <[email protected]>
@DrYak
Sync documentation to config schema
e8a6cab 
 - new sections for diversity
 - fixing trailing coma,
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github-actions bot commented Jan 6, 2022

MegaLinter status: ✅ SUCCESS

Descriptor Linter Files Fixed Errors Elapsed time
✅ BASH shellcheck 5 0 0.25s
✅ MARKDOWN markdownlint 5 1 0 1.03s
✅ PYTHON black 10 0 0 1.43s
✅ SNAKEMAKE snakefmt 18 0 0 8.39s

See errors details in artifact MegaLinter reports on GitHub Action page

@DrYak DrYak merged commit e8a6cab into master Jan 6, 2022
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@kpj kpj kpj approved these changes

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@DrYak @kpj