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Separate CI tests #350

Merged
merged 79 commits into from
Aug 17, 2023
Merged

Separate CI tests #350

merged 79 commits into from
Aug 17, 2023

Commits on Aug 9, 2023

  1. Seperate CI tests

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 9, 2023
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  2. Fix CI test

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 9, 2023
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  3. add test_malt

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 9, 2023
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  4. Prepare the database for motus

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 9, 2023
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  5. add database_motus.csv

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 9, 2023
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  6. Change the database

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 9, 2023
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  7. change the syntax in ci.yml

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 9, 2023
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  8. change mapping syntax in ci.yml

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 9, 2023
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  9. change mapping syntax in ci.yml

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 9, 2023
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  10. change mapping syntax in ci.yml

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 9, 2023
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Commits on Aug 10, 2023

  1. Update ci.yml 

    format the if condition
    @LilyAnderssonLee
    LilyAnderssonLee authored Aug 10, 2023
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  2. Update ci.yml

    @LilyAnderssonLee
    LilyAnderssonLee authored Aug 10, 2023
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  3. format

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 10, 2023
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  4. format

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 10, 2023
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  5. format

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 10, 2023
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  6. fix the database

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 10, 2023
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  7. remove test_full

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 10, 2023
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Commits on Aug 11, 2023

  1. move if into command action and put parameters into profile

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 11, 2023
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  2. Example of replacing old CI with 'alternate' tool CI test profile

    @jfy133
    jfy133 committed Aug 11, 2023
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  3. add test_adapterremoval.config

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 11, 2023
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  4. add test_bbduk.config

    @LilyAnderssonLee
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  5. add test_fastp.config

    @LilyAnderssonLee
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  6. add test_prinseqplusplus.config

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    LilyAnderssonLee committed Aug 11, 2023
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  7. change matrix parameters into tags

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 11, 2023
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  8. format

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 11, 2023
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  9. include test configs

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 11, 2023
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  10. format

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 11, 2023
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  11. Update ci.yml

    @LilyAnderssonLee
    LilyAnderssonLee authored Aug 11, 2023
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  12. Update ci.yml

    @LilyAnderssonLee
    LilyAnderssonLee authored Aug 11, 2023
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  13. Update ci.yml

    @LilyAnderssonLee
    LilyAnderssonLee authored Aug 11, 2023
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Commits on Aug 13, 2023

  1. format syntax

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 13, 2023
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Commits on Aug 14, 2023

  1. correct if syntax

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 14, 2023
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  2. correct if syntax

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 14, 2023
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  3. correct if syntax

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 14, 2023
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  4. correct if syntax

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 14, 2023
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  5. correct if syntax

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 14, 2023
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  6. correct if syntax

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 14, 2023
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  7. correct if syntax

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 14, 2023
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  8. correct if syntax

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 14, 2023
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  9. correct if syntax

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 14, 2023
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  10. correct if syntax

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 14, 2023
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  11. correct if syntax

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 14, 2023
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  12. correct if syntax

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 14, 2023
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  13. correct if syntax

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 14, 2023
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  14. correct if syntax

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 14, 2023
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  15. correct if syntax

    @LilyAnderssonLee
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  16. correct if syntax

    @LilyAnderssonLee
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  17. correct if syntax

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 14, 2023
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  18. correct if syntax

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 14, 2023
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  19. correct if syntax

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 14, 2023
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  20. correct if syntax

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 14, 2023
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Commits on Aug 15, 2023

  1. change bash block into one-line

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 15, 2023
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  2. Correct the path of test configs

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 15, 2023
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  3. correct the path of malt db

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 15, 2023
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  4. Correct malt db and remove test_full from CI test

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 15, 2023
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  5. use the samplesheet_shortreadsonly.csv

    @LilyAnderssonLee
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  6. use the samplesheet_shortreadsonly.csv

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 15, 2023
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  7. change the maximum memory for malt

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 15, 2023
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  8. change the maximum memory for malt

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 15, 2023
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  9. change test_malt.config according to test_nothing

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 15, 2023
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  10. Add github.workspace to the path of motus db

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 15, 2023
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  11. replace github.workspace by GITHUB_WORKSPACE

    @LilyAnderssonLee
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  12. correct motus db path

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 15, 2023
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  13. check github.worspace and GITHUB_WORKSHOP

    @LilyAnderssonLee
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  14. change the action version

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    LilyAnderssonLee committed Aug 15, 2023
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Commits on Aug 16, 2023

  1. move if condition outside of the action

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 16, 2023
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  2. remove test, test_full. test_nopreprocessing, test_nothing, test_nopr… 

    …ofiling
    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 16, 2023
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  3. remove extra params

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 16, 2023
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  4. add attempts into if conditon and remove Wandalen action

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 16, 2023
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  5. correct syntax of if

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 16, 2023
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  6. add basic test; add retry for failed jobs

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 16, 2023
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  7. Replace retry

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 16, 2023
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  8. Replace retry

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 16, 2023
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  9. Replace retry

    @LilyAnderssonLee
    LilyAnderssonLee committed Aug 16, 2023
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  10. Apply suggestions from code review

    @jfy133
    jfy133 authored Aug 16, 2023
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  11. Update conf/test_malt.config

    @jfy133
    jfy133 authored Aug 16, 2023
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  12. Update test_nopreprocessing.config

    @jfy133
    jfy133 authored Aug 16, 2023
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Commits on Aug 17, 2023

  1. Apply suggestions from code review

    @jfy133
    jfy133 authored Aug 17, 2023
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  2. Linting

    @jfy133
    jfy133 authored Aug 17, 2023
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