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Release - export file name improvements, GBS pipeline tweaks for ANOSPP, cell counting improvements for scRNA Core #1786

Merged
merged 80 commits into from
Jul 16, 2024
Merged

Release - export file name improvements, GBS pipeline tweaks for ANOSPP, cell counting improvements for scRNA Core #1786

merged 80 commits into from
Jul 16, 2024

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KatyTaylor
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Closes #

Changes proposed in this pull request

  • DPL-1031 - File name improvements (general enhancements to file export naming, plus specific changes to scRNA Core cell extraction file names)
  • Y24-136 config for the (not yet live) ANOSPP NDE pipeline
  • Y24-109 - Rework Limber documentation - Readme improvements
  • Y24-037 improvements to cell counting in scRNA Core cell extraction pipeline
  • Y24-041 more improvements to cell counting in scRNA Core cell extraction pipeline
  • Dependency updates
  • Y24-171 driver file pbmc pools to 10x chip (in preparation for scRNA Core cDNA prep pipeline - not yet live)

Instructions for Reviewers

[All PRs] - Confirm PR template filled
[Feature Branches] - Review code
[Production Merges to main]
    - Check story numbers included
    - Check for debug code
    - Check version

BenTopping and others added 30 commits June 28, 2024 10:09
@BenTopping
feat(exports): adds file name, parent labware barcode and prepend abi…
77dec63 
…lity to export filenames
@BenTopping
style: linted
38c7efe
@BenTopping
fix(exports): fixes labware human barcode reference for parent labware
adb165d
@andrewsparkes
renamed label template for use in ANOSPP and added ANOSPP pipleine an…
45d25f9 
…d purpose configs
@andrewsparkes
fix typo
f5d6d9e
@andrewsparkes
added new ANOSPP robot steps and modified existing GBS robot step to …
7a91f5d 
…accept ANOSPP plate
@andrewsparkes
renamed GBS config file and added ANOSPP plate into relationships to …
9d9c096 
…allow use when creating PCR1 plates
@andrewsparkes
fixed typos
f5550a9
@BenTopping
feat(exports): sets custom file name for hamilton pbmc plate files
e61f746
@BenTopping
Merge branch 'develop' of https://github.com/sanger/limber into DPL-1…
814fa41 
…031-file-name-improvements
@SHIV5T3R
Reordered steps for setting up both applications
51d2cbd
@SHIV5T3R
Added some detail about some of the jobs
0bcf198
@SHIV5T3R
Prettier
fd7439f
@BenTopping
docs(exports): typo fix and clarifys labware barcode behaviour in exp…
4aff9e3 
…orts yaml docs
@BenTopping
feat(exports): adds exports filename behaviour concern with unit tests
7fbdcb9
@BenTopping
refactor(exports-concern): cleans up tests and lints
f3c55a7
@andrewsparkes
Merge branch 'develop' into y24-136-anospp-pipeline-config
447a0ef
@depfu
Update webmock to version 3.23.1
acbf6c9
@KatyTaylor
Merge pull request #1752 from sanger/DPL-1031-file-name-improvements
d347ec1 
DPL-1031 - File name improvements
@andrewsparkes
Merge pull request #1755 from sanger/y24-136-anospp-pipeline-config
3954f0f 
Y24-136 anospp pipeline config
@yoldas
Remove download button for Cellaca Max 4 Count
c19aeff
@yoldas
Rename download button for Cellaca ALL Count to FIRST Count
78193d4
@yoldas
Rename export id for FIRST Count download
b89bca2
@yoldas
Rename CSV filename for Cellaca FIRST Count
d836467
@yoldas
Rename the template for Cellaca FIRST Count
bff0e90
@yoldas
Prepend labware barcode to Cellaca FIRST Count filename
f8cf397
@yoldas
Update export id of FIRST Count file
70bb4dd
@yoldas
Remove cellaca max 12 count export
815e63b
@yoldas
Remove cellaca max 6 count export
fde4a80
@yoldas
Remove cellaca max 4 count export
711e580
yoldas and others added 21 commits July 9, 2024 15:11
@yoldas
Merge pull request #1764 from sanger/depfu/update/webmock-3.23.1
a403053 
[ruby] Update webmock 3.23.0 → 3.23.1 (patch)
@yoldas
Add export hamilton_lrc_pbmc_pools_or_input_to_lrc_gem_x_5p_chip and …
273d4dc 
…configure prefixes
@yoldas
Add link Download Hamilton LRC PBMC Pools (or Input) to LRC GEM-X 5p …
326cf78 
…Chip CSV
@yoldas
Add template for driver file hamilton_lrc_pbmc_pools_or_input_to_lrc_…
1b8b679 
…gem_x_5p_chip.csv
@yoldas
Rename download id to hamilton_gem_x_5p_chip_loading
1532643
@yoldas
Rename export csv to hamilton_gem_x_5p_chip_loading
d2c0736
@yoldas
Rename template to hamilton_gem_x_5p_chip_loading
020127b
@yoldas
Rename workflow to scRNA Core GEM-X 5p Chip Loading
7588653
@yoldas
Remove vac tube barcode and sample name from csv
57e8bfe
@yoldas
Remove per aliquot loop; max 8 lines is expected to show the transfer
e12ed45
@yoldas
Rename export for lrc_pbmc_pools_or_input_to_lrc_gem_x_5p_chip
8e66084
@yoldas
Add test for rendering the export hamilton_gem_x_5p_chip_loading
6626a75
@yoldas
Exclude failed wells from the downloads
8f55dce
@yoldas
Add tests for downloads when wells are failed
1852b08
@yoldas
Merge pull request #1780 from sanger/y24-041-uat-update-4-cell-count-…
c6bc050 
…spot-checking

Y24 041 uat update 4 cell count spot checking
@yoldas
Merge pull request #1778 from sanger/1753-y24-171-driver-file-pbmc-po…
c5f3831 
…ols-to-10x-chip

1753 y24 171 driver file pbmc pools to 10x chip
@yoldas
Map destination wells to numbers in chip loading
163534c
@yoldas
Add test for mapping destination wells to numbers in chip loading
a947080
@yoldas
Rubocop
b655aa5
@yoldas
Merge pull request #1784 from sanger/y24-171-uat-update-driver-file-p…
3f90cc4 
…bmc-pools-to-10x-chip

Y24 171 uat update driver file pbmc pools to 10x chip
@KatyTaylor
new release version
e375ba9
@KatyTaylor KatyTaylor requested review from yoldas, andrewsparkes and sdjmchattie and removed request for sdjmchattie July 15, 2024 11:24
yoldas
yoldas approved these changes Jul 16, 2024
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Looks good.

@KatyTaylor KatyTaylor merged commit 19bfd8c into master Jul 16, 2024
24 checks passed
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@yoldas yoldas yoldas approved these changes

@sdjmchattie sdjmchattie sdjmchattie approved these changes

@andrewsparkes andrewsparkes Awaiting requested review from andrewsparkes

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6 participants
@KatyTaylor @yoldas @sdjmchattie @BenTopping @andrewsparkes @SHIV5T3R