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Merge develop with faster tests #199

Merged
merged 195 commits into from
May 31, 2024
Merged

Merge develop with faster tests #199

merged 195 commits into from
May 31, 2024

Commits on Apr 26, 2024

  1. Refactor HeatmapFiles class to include make_heatmaps property in desi… 

    …gn.py
    @alsmith151
    alsmith151 committed Apr 26, 2024
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  2. Refactor NonRNAOutput class in design.py to remove computed_field dec… 

    …orator
    @alsmith151
    alsmith151 committed Apr 26, 2024
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  3. fix: correct query function to provide both the ip and control if req… 

    …uested
    @alsmith151
    alsmith151 committed Apr 26, 2024
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  4. Refactor control lambda function in peak_call_chip.smk to allow null … 

    …control files
    @alsmith151
    alsmith151 committed Apr 26, 2024
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  5. Refactor query function in DesignIP class to return IPExperiment object

    @alsmith151
    alsmith151 committed Apr 26, 2024
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Commits on May 17, 2024

  1. Refactor FastqFile model to handle resolved and absolute paths

    @alsmith151
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Commits on May 19, 2024

  1. Refactor peak_call_grouped.smk to add runtime and mem resources for l… 

    …anceotron_no_input_consensus rule
    @alsmith151
    alsmith151 committed May 19, 2024
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  2. feat: Refactor pileup_norm.smk to use tile instead of tiles 

    The commit message suggests refactoring the `pileup_norm.smk` file to use the `tile` parameter instead of `tiles`.
    @alsmith151
    alsmith151 committed May 19, 2024
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Commits on May 23, 2024

  1. Merge branch 'fix-csaw-norm' into experimental

    @alsmith151
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  2. Merge branch 'fix-increase-grouped-peak-call-mem' into experimental

    @alsmith151
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  3. Merge branch 'fix-heatmaps-always-created' into experimental

    @alsmith151
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Commits on May 28, 2024

  1. fix typo design

    @CChahrour
    CChahrour committed May 28, 2024
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  2. fix tests fastq path

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    CChahrour committed May 28, 2024
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  3. fix merge in design

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  4. Merge branch 'develop' into experimental

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  5. Merge pull request #191 from alsmith151/experimental 

    Experimental
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  6. fix config

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  7. Merge branch 'develop' of https://github.com/alsmith151/SeqNado into … 

    …develop
    @CChahrour
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  8. reinstate snp into design

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  9. revert peaks and design

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  10. fixed typo from merge peak calls

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  11. simplify tests

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  12. update test order

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  13. correct test order

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  14. revert test order

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  15. split tests

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  16. increase cores for tests

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  17. revert single test

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  18. merge

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  19. merge develop to master

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  20. Merge branch 'master' into develop

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Commits on May 29, 2024

  1. remove codecov

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Commits on May 30, 2024

  1. subset data

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  2. parallel testing and cache conda

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  3. remove conda cache

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  4. matrix for parallel testing and cache conda and simg

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  5. fix restore conda env

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  6. fix error in extract env

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  7. fix conda tmp paths

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  8. add mkdir for conda extract

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  9. fix lack of pytest

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    CChahrour committed May 30, 2024
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  10. merge test and min envs

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  11. rename conda env

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    CChahrour committed May 30, 2024
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  12. fix mamba use for consistency

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    CChahrour committed May 30, 2024
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  13. activate mamba

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  14. separate out singularity from setup

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  15. remove setup as dependency in sing

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  16. add matrix for sing pull

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  17. update sing matrix

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  18. fix pull matrix

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  19. remove --output from apptainer pull

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  20. remove cache steps

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  21. check env install

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  22. explicit env naming

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  23. add symlink to env

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  24. fix paths to simg

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  25. installs mamba

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  26. activate conda env

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  27. explicit mamba path

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  28. fix test cmd

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  29. check conda env extract path

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  30. mk env dir

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  31. remove sing for now

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  32. make all conda

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  33. debug extract env

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  34. update env creation

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  35. update env create

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  36. verify env creation

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  37. revert to original conda

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  38. keep name of env as test

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  39. debug env path

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  40. update env create

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  41. remove activate env

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  42. cache dependencies

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  43. check seqnado v

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  44. add conda env to path

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  45. caching only conda

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  46. fix pytest cmd

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  47. add conditions for download

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  48. clean saving env

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  49. clean saving

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  50. add upload back

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  51. get cache output for test jobs

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  52. validate conda env

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  53. edit verify env

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  54. fix finding conda

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  55. clean up verify env

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  56. setup and test

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  57. remove cond case for verify env

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  58. remove source

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  59. simplify

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  60. update verify env

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  61. use setup env better

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  62. update caching

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  63. check conda envs

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  64. specify env path

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  65. update caching env

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  66. fix conda fields

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  67. fix conda cache

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  68. try test

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  69. conda envs from cache

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  70. change path to conda env

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  71. fix paths

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  72. fix mamba version

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  73. rmove bad options for setup env

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  74. remove conda channels

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  75. edit conda setup opts

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  76. add channels

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  77. remove updates

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  78. revert conda

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  79. update path to source

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  80. dont activate env

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  81. fix type in pytest cmd

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  82. add apptainer

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  83. typo in test matrix

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  84. tidy up

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  85. update names

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  86. revert tests but with matrix

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  87. add caching back

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  88. design for all assays

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  89. remove python setup

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  90. add debugging for config test

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  91. move design to pytest

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  92. cache conda

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  93. update pytest cmd

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  94. cache conda

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  95. separate pip cache

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  96. update tests

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  97. update pip cache

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  98. updates pytest cmd

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  99. fix config defaults

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  100. tidy up test names

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  101. remove paths from cache

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  102. set caches

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  103. try path for cache

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  104. combine caching

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  105. only install conda if cache not avail

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  106. restore tests

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  107. update env

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  108. remove conditions

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  109. save simgs as artefacts

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  110. access artefact images

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  111. move simg

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  112. set image files

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  113. set matrix images

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  114. remove prior load

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  115. exclude combos

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  116. fix pull cmd

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  117. fix simg paths

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  118. fix matrix

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  119. get list of simgs

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Commits on May 31, 2024

  1. get simgs

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  2. fix use simgs

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  3. pull no retries

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  4. get and extract simg

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  5. revert tests

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  6. remove sing pull dep

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  7. add apptainer

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  8. only setup apptainer for pipeline

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  9. cache id

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  10. cache simgs

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  11. specify imgs for each assay

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  12. fix cond assay

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  13. correct cond

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  14. clean tests

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  15. Merge pull request #195 from alsmith151/add-tests 

    Add parallel testing
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  16. Merge branch 'master' of https://github.com/alsmith151/SeqNado into d… 

    …evelop
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  17. add download and save simg

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  18. fix simg

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  19. keep pwsh

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  20. pull using bash

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  21. fix pull cmd

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  22. check for artefacts before pull

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  23. add remotes

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  24. cache simg

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  25. check caching

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  26. fix conditions for apptainer

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  27. change conditions for singularity

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  28. minor changes to check caching

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  29. change simg dir

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  30. add tmp to apptainer mounts

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  31. reduce sing cache names

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  32. only cache sing for pipeline

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  33. clean up cache

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  34. check cache

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  35. change cache dirs

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  36. update sing cache dir

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  37. mount apptainer cache in pytest and use tmp in workflow

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  38. remove simg names

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  39. correct apptainer cache dir in tests

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  40. Merge pull request #197 from alsmith151/fix-tests 

    Fix tests to run in minimal time
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  41. fix typo in workflow

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  42. Merge branch 'master' of https://github.com/alsmith151/SeqNado into d… 

    …evelop
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  43. merge error in workflow file

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  44. Merge branch 'master' into develop

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