Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[skip ci] Dev -> Master for 3.15.0 #1258

Open
wants to merge 541 commits into
base: master
Choose a base branch
from
Open

[skip ci] Dev -> Master for 3.15.0 #1258

wants to merge 541 commits into from
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Mar 11, 2024

  1. Replace check if no failure with success()

    @adamrtalbot @pinin4fjords
    adamrtalbot authored and pinin4fjords committed Mar 11, 2024
    Configuration menu
    Copy the full SHA
    5417f12 View commit details
    Browse the repository at this point in the history

  2. Update CHANGELOG.md

    @adamrtalbot
    adamrtalbot committed Mar 11, 2024
    Configuration menu
    Copy the full SHA
    fec6d8c View commit details
    Browse the repository at this point in the history

  3. Merge pull request #1228 from nf-core/readme_usage 

    Make README usage consistent with docs/usage.md
    @pinin4fjords
    pinin4fjords committed Mar 11, 2024
    Configuration menu
    Copy the full SHA
    e6d6efe View commit details
    Browse the repository at this point in the history

Commits on Mar 12, 2024

  1. Merge branch 'dev' into remove_tags.yml

    @drpatelh
    drpatelh committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    c5dbbf7 View commit details
    Browse the repository at this point in the history

  2. Merge pull request #1250 from adamrtalbot/remove_tags.yml 

    Remove all tags.yml files
    @drpatelh
    drpatelh committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    31037e1 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'dev' into new_testing_by_file_matrix

    @drpatelh
    drpatelh committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    d483646 View commit details
    Browse the repository at this point in the history

  4. SALMON tests keepDuplicates 

    Changes:
 - SALMON_INDEX will keep duplicates
 - summarizedexperiment will handle the missing transcripts
 - Version numbers checked in QUANTIFY_PSEUDO_ALIGNMENT subworkflow
    @adamrtalbot
    adamrtalbot committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    da29edb View commit details
    Browse the repository at this point in the history

  5. Merge branch 'dev' into nftest_rsem_merge_counts

    @maxulysse
    maxulysse committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    5af2b1d View commit details
    Browse the repository at this point in the history

  6. collect input files

    @maxulysse
    maxulysse committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    5ac549f View commit details
    Browse the repository at this point in the history

  7. Update modules/local/rsem_merge_counts/tests/main.nf.test 

    Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
    @maxulysse @adamrtalbot
    maxulysse and adamrtalbot committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    0f90900 View commit details
    Browse the repository at this point in the history

  8. forgot to commit this file deletion

    @maxulysse
    maxulysse committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    be63894 View commit details
    Browse the repository at this point in the history

  9. Merge branch 'dev' into nf-test_quantify_pseudoalignment

    @adamrtalbot
    adamrtalbot committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    63f71d7 View commit details
    Browse the repository at this point in the history

  10. Update modules/local/rsem_merge_counts/tests/main.nf.test

    @maxulysse
    maxulysse committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    49d8fff View commit details
    Browse the repository at this point in the history

  11. Merge pull request #1249 from nf-core/nftest_rsem_merge_counts 

    Include nf-tests for rsem_merge_counts module
    @adamrtalbot
    adamrtalbot committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    2e315c1 View commit details
    Browse the repository at this point in the history

  12. Merge branch 'dev' into nf-test_quantify_pseudoalignment

    @adamrtalbot
    adamrtalbot committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    35ff7ad View commit details
    Browse the repository at this point in the history

  13. Merge pull request #1246 from adamrtalbot/nf-test_quantify_pseudoalig… 

    …nment

nf-test quantify pseudoalignment
    @adamrtalbot
    adamrtalbot committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    e93915d View commit details
    Browse the repository at this point in the history

  14. Update CHANGELOG

    @drpatelh
    drpatelh committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    e4b1992 View commit details
    Browse the repository at this point in the history

  15. Merge pull request #1260 from drpatelh/fixes 

    Update CHANGELOG
    @drpatelh
    drpatelh committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    14e39d0 View commit details
    Browse the repository at this point in the history

  16. Add more tests for PREPARE_GENOME 

    Changes:
 - Adds a range of tests for lots of the PREPARE_GENOME parameters

Closes #1256
    @adamrtalbot
    adamrtalbot committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    0feb867 View commit details
    Browse the repository at this point in the history

  17. CHANGELOG

    @adamrtalbot
    adamrtalbot committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    af74016 View commit details
    Browse the repository at this point in the history

  18. Merge branch 'dev' into dev

    @adamrtalbot
    adamrtalbot committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    6c572c9 View commit details
    Browse the repository at this point in the history

  19. Remove existing tests that are duplicated by PUBLISH_GENOME tests

    @adamrtalbot
    adamrtalbot committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    7aeb72d View commit details
    Browse the repository at this point in the history

  20. Try to fix CI pipeline AGAIN

    @adamrtalbot
    adamrtalbot committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    1795f8e View commit details
    Browse the repository at this point in the history

  21. Check for empty list

    @adamrtalbot
    adamrtalbot committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    dcec9db View commit details
    Browse the repository at this point in the history

  22. Revert needs statement

    @adamrtalbot
    adamrtalbot committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    8789e4f View commit details
    Browse the repository at this point in the history

  23. Trying something else...

    @adamrtalbot
    adamrtalbot committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    21c23e2 View commit details
    Browse the repository at this point in the history

  24. Add everything to test dep

    @adamrtalbot
    adamrtalbot committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    0df628a View commit details
    Browse the repository at this point in the history

Commits on Mar 13, 2024

  1. Merge pull request #1262 from adamrtalbot/fix_ci_test_deps_2 

    Try to fix CI pipeline AGAIN
    @adamrtalbot
    adamrtalbot committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    8858f7f View commit details
    Browse the repository at this point in the history

  2. Fixup: Add GHA files back into include statement of Github workflow c… 

    …hange detection
    @adamrtalbot
    adamrtalbot committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    2de9854 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'dev' into dev

    @adamrtalbot
    adamrtalbot committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    5043521 View commit details
    Browse the repository at this point in the history

  4. Add missing software updates to CHANGELOG

    @drpatelh
    drpatelh committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    40a64b3 View commit details
    Browse the repository at this point in the history

  5. Move aliased bedtools genomecov selectors to main workflow config

    @drpatelh
    drpatelh committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    3c6317b View commit details
    Browse the repository at this point in the history

  6. Syntax updates

    @drpatelh
    drpatelh committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    7e06185 View commit details
    Browse the repository at this point in the history

  7. Rename checkSamplesAreConsistent to checkSamplesAfterGrouping

    @drpatelh
    drpatelh committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    e060706 View commit details
    Browse the repository at this point in the history

  8. Update CHANGELOG

    @drpatelh
    drpatelh committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    379decc View commit details
    Browse the repository at this point in the history

  9. Fix pre-commit lint

    @drpatelh
    drpatelh committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    798acea View commit details
    Browse the repository at this point in the history

  10. Update tests to omit snapshot of variable files

    @adamrtalbot
    adamrtalbot committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    f8887de View commit details
    Browse the repository at this point in the history

  11. Revert renaming UMITOOLS_PREPAREFORSALMON to UMITOOLS_PREPAREFORRSEM

    @drpatelh
    drpatelh committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    9584d70 View commit details
    Browse the repository at this point in the history

  12. Merge pull request #1265 from drpatelh/fixes 

    Small updates noticed during code review
    @drpatelh
    drpatelh committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    bf7883e View commit details
    Browse the repository at this point in the history

  13. Delete unecessary tags from nt.test files for modules

    @drpatelh
    drpatelh committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    155c635 View commit details
    Browse the repository at this point in the history

  14. Delete unecessary tags from nt.test files for subworkflows

    @drpatelh
    drpatelh committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    67603db View commit details
    Browse the repository at this point in the history

  15. Update CHANGELOG

    @drpatelh
    drpatelh committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    7b63973 View commit details
    Browse the repository at this point in the history

  16. Merge pull request #1266 from drpatelh/fixes 

    Delete unecessary tags from nf.test files for modules and subworkflows
    @drpatelh
    drpatelh committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    9c6d145 View commit details
    Browse the repository at this point in the history

Commits on Mar 14, 2024

  1. Remove indexing on output channels

    @adamrtalbot
    adamrtalbot committed Mar 14, 2024
    Configuration menu
    Copy the full SHA
    c169f35 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'dev' into dev

    @pinin4fjords
    pinin4fjords committed Mar 14, 2024
    Configuration menu
    Copy the full SHA
    cf06e96 View commit details
    Browse the repository at this point in the history

  3. Merge pull request #1261 from adamrtalbot/dev 

    Add more tests for PREPARE_GENOME
    @adamrtalbot
    adamrtalbot committed Mar 14, 2024
    Configuration menu
    Copy the full SHA
    6527469 View commit details
    Browse the repository at this point in the history

Commits on Mar 15, 2024

  1. Update snap

    @adamrtalbot
    adamrtalbot committed Mar 15, 2024
    Configuration menu
    Copy the full SHA
    4d1a32e View commit details
    Browse the repository at this point in the history

  2. Bug fixes and improvements

    @adamrtalbot
    adamrtalbot committed Mar 15, 2024
    Configuration menu
    Copy the full SHA
    f400865 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'dev' into new_testing_by_file_matrix

    @adamrtalbot
    adamrtalbot committed Mar 15, 2024
    Configuration menu
    Copy the full SHA
    ed96314 View commit details
    Browse the repository at this point in the history

  4. Remove R from Snap

    @adamrtalbot
    adamrtalbot committed Mar 15, 2024
    Configuration menu
    Copy the full SHA
    48e154a View commit details
    Browse the repository at this point in the history

Commits on Mar 18, 2024

  1. Merge pull request #1264 from nf-core/fixup-add-gha-back-into-incldue 

    Fixup: Add GHA files back into include statement of Github workflow change detection
    @adamrtalbot
    adamrtalbot committed Mar 18, 2024
    Configuration menu
    Copy the full SHA
    a5a409d View commit details
    Browse the repository at this point in the history

Commits on Mar 19, 2024

  1. Update trimming subworkflow to include more tests

    @adamrtalbot
    adamrtalbot committed Mar 19, 2024
    Configuration menu
    Copy the full SHA
    3d73f2c View commit details
    Browse the repository at this point in the history

  2. Bump subworkflow version

    @adamrtalbot
    adamrtalbot committed Mar 19, 2024
    Configuration menu
    Copy the full SHA
    2179ef9 View commit details
    Browse the repository at this point in the history

Commits on Mar 20, 2024

  1. move getGenomeAttribute to main.nf

    @maxulysse
    maxulysse committed Mar 20, 2024
    Configuration menu
    Copy the full SHA
    c84a589 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'dev' into getGenomeAttribute

    @maxulysse
    maxulysse committed Mar 20, 2024
    Configuration menu
    Copy the full SHA
    1ec2cfa View commit details
    Browse the repository at this point in the history

Commits on Mar 21, 2024

  1. Add direct replacements for existing tests 

    Additions:
- Runs simple tests for workflows
- Directly replaces existing tests in .github/workflows
- No checks for outputs or contents
    @adamrtalbot
    adamrtalbot committed Mar 21, 2024
    Configuration menu
    Copy the full SHA
    c49f446 View commit details
    Browse the repository at this point in the history

  2. Reorganised into discrete folders

    @adamrtalbot
    adamrtalbot committed Mar 21, 2024
    Configuration menu
    Copy the full SHA
    4d9acbb View commit details
    Browse the repository at this point in the history

  3. More all tests into subdirectory for more organisation

    @adamrtalbot
    adamrtalbot committed Mar 21, 2024
    Configuration menu
    Copy the full SHA
    08e89eb View commit details
    Browse the repository at this point in the history

  4. remove redundant tests

    @adamrtalbot
    adamrtalbot committed Mar 21, 2024
    Configuration menu
    Copy the full SHA
    967563b View commit details
    Browse the repository at this point in the history

  5. Remove invalid dependencies from GHA confirm-pass

    @adamrtalbot
    adamrtalbot committed Mar 21, 2024
    Configuration menu
    Copy the full SHA
    c2861cc View commit details
    Browse the repository at this point in the history

  6. Correct pipeline test path

    @adamrtalbot
    adamrtalbot committed Mar 21, 2024
    Configuration menu
    Copy the full SHA
    c00917c View commit details
    Browse the repository at this point in the history

  7. Relative path AGAIN

    @adamrtalbot
    adamrtalbot committed Mar 21, 2024
    Configuration menu
    Copy the full SHA
    622d8c6 View commit details
    Browse the repository at this point in the history

Commits on Mar 22, 2024

  1. Merge pull request #1271 from adamrtalbot/update_trimming_subworkflow 

    Update trimming subworkflow to include more tests
    @adamrtalbot
    adamrtalbot committed Mar 22, 2024
    Configuration menu
    Copy the full SHA
    1817d14 View commit details
    Browse the repository at this point in the history

  2. Update bam_markduplicates_picard subworkflow

    @adamrtalbot
    adamrtalbot committed Mar 22, 2024
    Configuration menu
    Copy the full SHA
    e79a587 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'dev' into update_bam_markduplicates_picard

    @adamrtalbot
    adamrtalbot committed Mar 22, 2024
    Configuration menu
    Copy the full SHA
    18debd9 View commit details
    Browse the repository at this point in the history

  4. Merge branch 'dev' into pipeline_level_tests_simple

    @adamrtalbot
    adamrtalbot committed Mar 22, 2024
    Configuration menu
    Copy the full SHA
    fe8673b View commit details
    Browse the repository at this point in the history

  5. Merge branch 'dev' into new_testing_by_file_matrix

    @adamrtalbot
    adamrtalbot committed Mar 22, 2024
    Configuration menu
    Copy the full SHA
    de83666 View commit details
    Browse the repository at this point in the history

Commits on Apr 3, 2024

  1. Delocalise pseudo quant workflow

    @pinin4fjords
    pinin4fjords committed Apr 3, 2024
    Configuration menu
    Copy the full SHA
    c544945 View commit details
    Browse the repository at this point in the history

  2. Update changelog

    @pinin4fjords
    pinin4fjords committed Apr 3, 2024
    Configuration menu
    Copy the full SHA
    9fcad99 View commit details
    Browse the repository at this point in the history

Commits on Apr 4, 2024

  1. Bump tximport for reproducible versions

    @pinin4fjords
    pinin4fjords committed Apr 4, 2024
    Configuration menu
    Copy the full SHA
    cf5a43b View commit details
    Browse the repository at this point in the history

  2. Bump subworkflow for linting

    @pinin4fjords
    pinin4fjords committed Apr 4, 2024
    Configuration menu
    Copy the full SHA
    2ba5358 View commit details
    Browse the repository at this point in the history

  3. Restore missing files

    @pinin4fjords
    pinin4fjords committed Apr 4, 2024
    Configuration menu
    Copy the full SHA
    e54864b View commit details
    Browse the repository at this point in the history

  4. Strip tags.ymls

    @pinin4fjords
    pinin4fjords committed Apr 4, 2024
    Configuration menu
    Copy the full SHA
    fc33902 View commit details
    Browse the repository at this point in the history

  5. Merge pull request #1278 from nf-core/delocalise_quant 

    Delocalise pseudo quant workflow
    @pinin4fjords
    pinin4fjords committed Apr 4, 2024
    Configuration menu
    Copy the full SHA
    13ac9c5 View commit details
    Browse the repository at this point in the history

Commits on Apr 5, 2024

  1. Merge pull request #1274 from adamrtalbot/update_bam_markduplicates_p… 

    …icard

Update bam_markduplicates_picard subworkflow
    @adamrtalbot
    adamrtalbot committed Apr 5, 2024
    Configuration menu
    Copy the full SHA
    f6fa12c View commit details
    Browse the repository at this point in the history

  2. Merge branch 'dev' into pipeline_level_tests_simple

    @adamrtalbot
    adamrtalbot committed Apr 5, 2024
    Configuration menu
    Copy the full SHA
    bcc1a00 View commit details
    Browse the repository at this point in the history

Commits on Apr 9, 2024

  1. Remove r-base from software versions

    @adamrtalbot
    adamrtalbot committed Apr 9, 2024
    Configuration menu
    Copy the full SHA
    e01e195 View commit details
    Browse the repository at this point in the history

  2. Move repo tests config to tests/config

    @adamrtalbot
    adamrtalbot committed Apr 9, 2024
    Configuration menu
    Copy the full SHA
    6e6a254 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'dev' into new_testing_by_file_matrix

    @adamrtalbot
    adamrtalbot committed Apr 9, 2024
    Configuration menu
    Copy the full SHA
    905433a View commit details
    Browse the repository at this point in the history

  4. Add test config

    @adamrtalbot
    adamrtalbot committed Apr 9, 2024
    Configuration menu
    Copy the full SHA
    76473d2 View commit details
    Browse the repository at this point in the history

  5. Merge branch 'dev' into getGenomeAttribute

    @maxulysse
    maxulysse committed Apr 9, 2024
    Configuration menu
    Copy the full SHA
    9c0e8eb View commit details
    Browse the repository at this point in the history

  6. Merge pull request #1272 from nf-core/pipeline_level_tests_simple 

    Simple pipeline level nf-tests
    @adamrtalbot
    adamrtalbot committed Apr 9, 2024
    Configuration menu
    Copy the full SHA
    943e271 View commit details
    Browse the repository at this point in the history

  7. Merge branch 'dev' into new_testing_by_file_matrix

    @adamrtalbot
    adamrtalbot committed Apr 9, 2024
    Configuration menu
    Copy the full SHA
    f244455 View commit details
    Browse the repository at this point in the history

  8. Add psueudoaligner pipeline level tests to test suite

    @adamrtalbot
    adamrtalbot committed Apr 9, 2024
    Configuration menu
    Copy the full SHA
    6f3b925 View commit details
    Browse the repository at this point in the history

  9. CI fixup

    @adamrtalbot
    adamrtalbot committed Apr 9, 2024
    Configuration menu
    Copy the full SHA
    eea41e7 View commit details
    Browse the repository at this point in the history

  10. Merge pull request #1253 from adamrtalbot/new_testing_by_file_matrix 

    Add new testing strategy based on nf-test files
    @adamrtalbot
    adamrtalbot committed Apr 9, 2024
    Configuration menu
    Copy the full SHA
    05c12ca View commit details
    Browse the repository at this point in the history

  11. Merge branch 'dev' into pseudo_aligners_nftest

    @adamrtalbot
    adamrtalbot committed Apr 9, 2024
    Configuration menu
    Copy the full SHA
    a7389c0 View commit details
    Browse the repository at this point in the history

Commits on Apr 10, 2024

  1. Correct snaps for pseudoalignment

    @adamrtalbot
    adamrtalbot committed Apr 10, 2024
    Configuration menu
    Copy the full SHA
    4299d47 View commit details
    Browse the repository at this point in the history

  2. Merge pull request #1279 from adamrtalbot/pseudo_aligners_nftest 

    Add psueudoaligner pipeline level tests to test suite
    @adamrtalbot
    adamrtalbot committed Apr 10, 2024
    Configuration menu
    Copy the full SHA
    f3aec8b View commit details
    Browse the repository at this point in the history

  3. Reorganise pipeline tests into flat structure 

    Changes:
 - Move all test files from tests/tests/ to test/*.nf.test
 - Makes structure more flat and discovery easier at the cost of looking more untidy.
 - To be discussed in PR!
    @adamrtalbot
    adamrtalbot committed Apr 10, 2024
    Configuration menu
    Copy the full SHA
    d6206f4 View commit details
    Browse the repository at this point in the history

  4. Use profile test --input parameter

    @adamrtalbot
    adamrtalbot committed Apr 10, 2024
    Configuration menu
    Copy the full SHA
    d1c636a View commit details
    Browse the repository at this point in the history

  5. indentation

    @adamrtalbot
    adamrtalbot committed Apr 10, 2024
    Configuration menu
    Copy the full SHA
    c259f30 View commit details
    Browse the repository at this point in the history

  6. Merge pull request #1280 from adamrtalbot/dev 

    Reorganise pipeline tests into flat structure
    @adamrtalbot
    adamrtalbot committed Apr 10, 2024
    Configuration menu
    Copy the full SHA
    5833810 View commit details
    Browse the repository at this point in the history

  7. Fixup CHANGELOG

    @adamrtalbot
    adamrtalbot committed Apr 10, 2024
    Configuration menu
    Copy the full SHA
    7323bb1 View commit details
    Browse the repository at this point in the history

  8. Increase contents of default.main.nf.test.snap 

    Changes:
 - Adds output files to nf-test snapshot
 - Used files that are important for downstream analysis to ensure that the snapshot is useful for testing
 - Should help stability of pipeline
    @adamrtalbot
    adamrtalbot committed Apr 10, 2024
    Configuration menu
    Copy the full SHA
    2f42e75 View commit details
    Browse the repository at this point in the history

  9. Merge pull request #1282 from adamrtalbot/fixup_changelog_error 

    Fix CHANGELOG error
    @maxulysse
    maxulysse committed Apr 10, 2024
    Configuration menu
    Copy the full SHA
    9e4cf57 View commit details
    Browse the repository at this point in the history

  10. CHANGELOG

    @adamrtalbot
    adamrtalbot committed Apr 10, 2024
    Configuration menu
    Copy the full SHA
    651c755 View commit details
    Browse the repository at this point in the history

  11. Merge branch 'dev' into increase_coverage_of_default_test_snapshot

    @adamrtalbot
    adamrtalbot committed Apr 10, 2024
    Configuration menu
    Copy the full SHA
    abb3afb View commit details
    Browse the repository at this point in the history

Commits on Apr 11, 2024

  1. Remove variable files from default pipeline snapshot

    @adamrtalbot
    adamrtalbot committed Apr 11, 2024
    Configuration menu
    Copy the full SHA
    9d281ab View commit details
    Browse the repository at this point in the history

  2. update snap

    @adamrtalbot
    adamrtalbot committed Apr 11, 2024
    Configuration menu
    Copy the full SHA
    4c0ac4c View commit details
    Browse the repository at this point in the history

  3. Merge branch 'dev' into getGenomeAttribute

    @maxulysse
    maxulysse committed Apr 11, 2024
    Configuration menu
    Copy the full SHA
    71ef0f5 View commit details
    Browse the repository at this point in the history

  4. Remove more from snaps

    @adamrtalbot
    adamrtalbot committed Apr 11, 2024
    Configuration menu
    Copy the full SHA
    b903195 View commit details
    Browse the repository at this point in the history

Commits on Apr 12, 2024

  1. feat(igenomes): update name as in template

    @maxulysse
    maxulysse committed Apr 12, 2024
    Configuration menu
    Copy the full SHA
    d62e208 View commit details
    Browse the repository at this point in the history

  2. feat(references): fix usage of igenomes references

    @maxulysse
    maxulysse committed Apr 12, 2024
    Configuration menu
    Copy the full SHA
    a54300a View commit details
    Browse the repository at this point in the history

  3. no need for key

    @maxulysse
    maxulysse committed Apr 12, 2024
    Configuration menu
    Copy the full SHA
    8f3603a View commit details
    Browse the repository at this point in the history

  4. Merge pull request #1283 from adamrtalbot/increase_coverage_of_defaul… 

    …t_test_snapshot

Increase contents of default.main.nf.test.snap
    @adamrtalbot
    adamrtalbot committed Apr 12, 2024
    Configuration menu
    Copy the full SHA
    d129b5a View commit details
    Browse the repository at this point in the history

  5. remove tests for functionned removed

    @maxulysse
    maxulysse committed Apr 12, 2024
    Configuration menu
    Copy the full SHA
    17767e1 View commit details
    Browse the repository at this point in the history

Commits on Apr 16, 2024

  1. Improve the extra_args parameter consolidation so it can override pre… 

    …sets from the config.
    @MatthiasZepper
    MatthiasZepper committed Apr 16, 2024
    Configuration menu
    Copy the full SHA
    fbaef17 View commit details
    Browse the repository at this point in the history

  2. Changelog update.

    @MatthiasZepper
    MatthiasZepper committed Apr 16, 2024
    Configuration menu
    Copy the full SHA
    0d7e0f5 View commit details
    Browse the repository at this point in the history

  3. Implement Jonathan Manning's map-method for extra argument consolidat… 

    …ion for the local STAR alignment subworkflow.
    @MatthiasZepper
    MatthiasZepper committed Apr 16, 2024
    Configuration menu
    Copy the full SHA
    934019e View commit details
    Browse the repository at this point in the history

  4. Implement Jonathan Manning's map-method for extra argument consolidat… 

    …ion for the FastQC-UMItools-Trimgalore subworkflow..
    @MatthiasZepper
    MatthiasZepper committed Apr 16, 2024
    Configuration menu
    Copy the full SHA
    8027585 View commit details
    Browse the repository at this point in the history

Commits on Apr 17, 2024

  1. Apply @pinin4fjords (Jonathan Manning)'s suggestions from code review 

    Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io>
    @MatthiasZepper @pinin4fjords
    MatthiasZepper and pinin4fjords committed Apr 17, 2024
    Configuration menu
    Copy the full SHA
    6ab2e44 View commit details
    Browse the repository at this point in the history

Commits on Apr 18, 2024

  1. Merge pull request #1248 from MatthiasZepper/ExtraArgsConsolidation 

    Improved ext.args consolidation for STAR and TRIMGALORE
    @MatthiasZepper
    MatthiasZepper committed Apr 18, 2024
    Configuration menu
    Copy the full SHA
    dcd5659 View commit details
    Browse the repository at this point in the history

Commits on Apr 22, 2024

  1. Merge pull request #1252 from maxulysse/getGenomeAttribute 

    Fix genomeAttribute usage
    @maxulysse
    maxulysse committed Apr 22, 2024
    Configuration menu
    Copy the full SHA
    b67141d View commit details
    Browse the repository at this point in the history

Commits on May 6, 2024

  1. fix(subworkflow): update utils_nfcore_pipeline

    @maxulysse
    maxulysse committed May 6, 2024
    Configuration menu
    Copy the full SHA
    6ca35a9 View commit details
    Browse the repository at this point in the history

  2. Merge pull request #1293 from maxulysse/utils_nfcore_pipeline 

    fix(subworkflow): update utils_nfcore_pipeline
    @maxulysse
    maxulysse committed May 6, 2024
    Configuration menu
    Copy the full SHA
    14fa853 View commit details
    Browse the repository at this point in the history

Commits on May 8, 2024

  1. Template update for nf-core/tools version 2.14.0

    @nf-core-bot
    nf-core-bot committed May 8, 2024
    Configuration menu
    Copy the full SHA
    e99cdbc View commit details
    Browse the repository at this point in the history

Commits on May 9, 2024

  1. Template update for nf-core/tools version 2.14.1

    @nf-core-bot
    nf-core-bot committed May 9, 2024
    Configuration menu
    Copy the full SHA
    eecf64e View commit details
    Browse the repository at this point in the history

Commits on May 13, 2024

  1. Fix merge conflicts

    @drpatelh
    drpatelh committed May 13, 2024
    Configuration menu
    Copy the full SHA
    31d8b23 View commit details
    Browse the repository at this point in the history

  2. Update CHANGELOG

    @drpatelh
    drpatelh committed May 13, 2024
    Configuration menu
    Copy the full SHA
    27b1503 View commit details
    Browse the repository at this point in the history

  3. Merge pull request #1297 from nf-core/nf-core-template-merge-2.14.1 

    Important! Template update for nf-core/tools v2.14.1
    @drpatelh
    drpatelh committed May 13, 2024
    Configuration menu
    Copy the full SHA
    431edb0 View commit details
    Browse the repository at this point in the history

Commits on May 16, 2024

  1. Update tximport subworkflow and module

    @pinin4fjords
    pinin4fjords committed May 16, 2024
    Configuration menu
    Copy the full SHA
    28493ee View commit details
    Browse the repository at this point in the history

  2. Update Changelog

    @pinin4fjords
    pinin4fjords committed May 16, 2024
    Configuration menu
    Copy the full SHA
    1374149 View commit details
    Browse the repository at this point in the history

  3. Merge pull request #1302 from nf-core/tximport_fix_missing_files 

    Add missing files from Tximport processing
    @pinin4fjords
    pinin4fjords committed May 16, 2024
    Configuration menu
    Copy the full SHA
    e0b41b4 View commit details
    Browse the repository at this point in the history

Commits on May 28, 2024

  1. Remove extra unnecessary tpm outputs

    @pinin4fjords
    pinin4fjords committed May 28, 2024
    Configuration menu
    Copy the full SHA
    4e719dc View commit details
    Browse the repository at this point in the history

  2. Update CHANGELOG

    @pinin4fjords
    pinin4fjords committed May 28, 2024
    Configuration menu
    Copy the full SHA
    deded7b View commit details
    Browse the repository at this point in the history

  3. Update CHANGELOG

    @pinin4fjords
    pinin4fjords committed May 28, 2024
    Configuration menu
    Copy the full SHA
    2a86507 View commit details
    Browse the repository at this point in the history

Commits on May 29, 2024

  1. Merge pull request #1304 from nf-core/no_extra_tpms 

    Remove redundant gene TPM outputs
    @pinin4fjords
    pinin4fjords committed May 29, 2024
    Configuration menu
    Copy the full SHA
    21095f3 View commit details
    Browse the repository at this point in the history

  2. Check RSeQC strandedness without reference to undetermined

    @pinin4fjords
    pinin4fjords committed May 29, 2024
    Configuration menu
    Copy the full SHA
    0cfb662 View commit details
    Browse the repository at this point in the history

  3. Update subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf 

    Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
    @pinin4fjords @drpatelh
    pinin4fjords and drpatelh committed May 29, 2024
    Configuration menu
    Copy the full SHA
    5ce89ae View commit details
    Browse the repository at this point in the history

  4. close #1095

    @maxulysse
    maxulysse committed May 29, 2024
    Configuration menu
    Copy the full SHA
    afa81b4 View commit details
    Browse the repository at this point in the history

Commits on May 30, 2024

  1. Document FASTP sampling

    @pinin4fjords
    pinin4fjords committed May 30, 2024
    Configuration menu
    Copy the full SHA
    b044fe2 View commit details
    Browse the repository at this point in the history

  2. Update CHANGELOG

    @pinin4fjords
    pinin4fjords committed May 30, 2024
    Configuration menu
    Copy the full SHA
    cdc8f53 View commit details
    Browse the repository at this point in the history

  3. Add missing subworkflow config import

    @pinin4fjords
    pinin4fjords committed May 30, 2024
    Configuration menu
    Copy the full SHA
    01c76fe View commit details
    Browse the repository at this point in the history

  4. correctly reference quantification subworkflow config

    @pinin4fjords
    pinin4fjords committed May 30, 2024
    Configuration menu
    Copy the full SHA
    645abe4 View commit details
    Browse the repository at this point in the history

  5. update changelog

    @pinin4fjords
    pinin4fjords committed May 30, 2024
    Configuration menu
    Copy the full SHA
    5bef11b View commit details
    Browse the repository at this point in the history

Commits on May 31, 2024

  1. Fix issues with unzipping of GTF/ GFF files

    @pinin4fjords
    pinin4fjords committed May 31, 2024
    Configuration menu
    Copy the full SHA
    eef9910 View commit details
    Browse the repository at this point in the history

  2. Update changelog

    @pinin4fjords
    pinin4fjords committed May 31, 2024
    Configuration menu
    Copy the full SHA
    11b68dd View commit details
    Browse the repository at this point in the history

  3. Same for other zipped reference inputs

    @pinin4fjords
    pinin4fjords committed May 31, 2024
    Configuration menu
    Copy the full SHA
    f018a0c View commit details
    Browse the repository at this point in the history

Commits on Jun 12, 2024

  1. fix strand message

    @pinin4fjords
    pinin4fjords committed Jun 12, 2024
    Configuration menu
    Copy the full SHA
    26a329b View commit details
    Browse the repository at this point in the history

  2. Strip problematic ifEmpty()

    @pinin4fjords
    pinin4fjords committed Jun 12, 2024
    Configuration menu
    Copy the full SHA
    865a9f1 View commit details
    Browse the repository at this point in the history

  3. Update CHANGELOG

    @pinin4fjords
    pinin4fjords committed Jun 12, 2024
    Configuration menu
    Copy the full SHA
    a8eb811 View commit details
    Browse the repository at this point in the history

  4. Merge pull request #1317 from nf-core/strip_ifempty 

    Strip problematic ifEmpty()
    @pinin4fjords
    pinin4fjords committed Jun 12, 2024
    Configuration menu
    Copy the full SHA
    e277e3e View commit details
    Browse the repository at this point in the history

Commits on Jun 13, 2024

  1. Merge branch 'dev' into improve_rseqc_strandedness

    @pinin4fjords
    pinin4fjords committed Jun 13, 2024
    Configuration menu
    Copy the full SHA
    7a20206 View commit details
    Browse the repository at this point in the history

Commits on Jun 14, 2024

  1. Update Salmon

    @pinin4fjords
    pinin4fjords committed Jun 14, 2024
    Configuration menu
    Copy the full SHA
    4c4afd0 View commit details
    Browse the repository at this point in the history

  2. Add strandedness detection threshold parameter

    @pinin4fjords
    pinin4fjords committed Jun 14, 2024
    Configuration menu
    Copy the full SHA
    2a5414c View commit details
    Browse the repository at this point in the history

  3. Add a consistent library type check between Salmon and RSeQC. Make th… 

    …e strand check results standard
    @pinin4fjords
    pinin4fjords committed Jun 14, 2024
    Configuration menu
    Copy the full SHA
    8ccffc9 View commit details
    Browse the repository at this point in the history

  4. Amend for undetermined

    @pinin4fjords
    pinin4fjords committed Jun 14, 2024
    Configuration menu
    Copy the full SHA
    c6b91a9 View commit details
    Browse the repository at this point in the history

  5. Constraint strand detection threshold

    @pinin4fjords
    pinin4fjords committed Jun 14, 2024
    Configuration menu
    Copy the full SHA
    ab0c62b View commit details
    Browse the repository at this point in the history

  6. Consistent defaults

    @pinin4fjords
    pinin4fjords committed Jun 14, 2024
    Configuration menu
    Copy the full SHA
    38bdb9e View commit details
    Browse the repository at this point in the history

Commits on Jun 17, 2024

  1. Reinstate onComplete messages

    @pinin4fjords
    pinin4fjords committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    db2aaa8 View commit details
    Browse the repository at this point in the history

  2. Appease linting

    @pinin4fjords
    pinin4fjords committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    cacebad View commit details
    Browse the repository at this point in the history

  3. update CHANGELOG

    @pinin4fjords
    pinin4fjords committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    2a38654 View commit details
    Browse the repository at this point in the history

  4. strandedness failure doesn't skip

    @pinin4fjords
    pinin4fjords committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    ec65b3e View commit details
    Browse the repository at this point in the history

  5. Fix PIPELINE_COMPLETEION test

    @pinin4fjords
    pinin4fjords committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    74c4fe3 View commit details
    Browse the repository at this point in the history

  6. Don't need non-custom completion summary

    @pinin4fjords
    pinin4fjords committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    22cd0f8 View commit details
    Browse the repository at this point in the history

  7. Merge pull request #1319 from nf-core/reinstate_oncomplete 

    Reinstate oncomplete error messages
    @pinin4fjords
    pinin4fjords committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    1f19aba View commit details
    Browse the repository at this point in the history

  8. Merge branch 'dev' into improve_rseqc_strandedness

    @pinin4fjords
    pinin4fjords committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    cb54dc2 View commit details
    Browse the repository at this point in the history

  9. Fix up after merge

    @pinin4fjords
    pinin4fjords committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    9aadd4a View commit details
    Browse the repository at this point in the history

  10. Fix for linting

    @pinin4fjords
    pinin4fjords committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    82724b8 View commit details
    Browse the repository at this point in the history

  11. update CHANGELOG

    @pinin4fjords
    pinin4fjords committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    c4d3535 View commit details
    Browse the repository at this point in the history

  12. Fix the fix

    @pinin4fjords
    pinin4fjords committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    9dd6d6d View commit details
    Browse the repository at this point in the history

  13. fix typos

    @pinin4fjords
    pinin4fjords committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    451cb64 View commit details
    Browse the repository at this point in the history

  14. [automated] Fix linting with Prettier

    @nf-core-bot
    nf-core-bot committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    3df6ec8 View commit details
    Browse the repository at this point in the history

  15. Fix module lint error

    @pinin4fjords
    pinin4fjords committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    007bde2 View commit details
    Browse the repository at this point in the history

  16. revert config changed in error

    @pinin4fjords
    pinin4fjords committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    002ebbd View commit details
    Browse the repository at this point in the history

  17. Merge branch 'improve_rseqc_strandedness' of github.com:nf-core/rnase… 

    …q into improve_rseqc_strandedness
    @pinin4fjords
    pinin4fjords committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    465be1f View commit details
    Browse the repository at this point in the history

  18. Fix conditionality

    @pinin4fjords
    pinin4fjords committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    1977f6d View commit details
    Browse the repository at this point in the history

Commits on Jun 18, 2024

  1. Clarify stranded/ unstraded at library level, include other library t… 

    …ypes in strand totals
    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    bc6189f View commit details
    Browse the repository at this point in the history

  2. Merge branch 'dev' into fix_salmon_args

    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    ef7fc82 View commit details
    Browse the repository at this point in the history

  3. Allow for missing keys in salmon library counts for testing

    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    62ed423 View commit details
    Browse the repository at this point in the history

  4. Fix function tests

    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    b4760ce View commit details
    Browse the repository at this point in the history

  5. Update ci.yml

    @adamrtalbot
    adamrtalbot committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    1bddbfb View commit details
    Browse the repository at this point in the history

  6. Auto updating snapshot broke things for unaffected tests. So manually… 

    … insert snapshots from the only tests I do want to update
    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    2ded8c0 View commit details
    Browse the repository at this point in the history

  7. Merge branch 'dev' into fix_gtf_unzip

    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    25aef1d View commit details
    Browse the repository at this point in the history

  8. Merge pull request #1310 from nf-core/fix_salmon_args 

    Reinstate pseudoalignment subworkflow config
    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    fa34ca6 View commit details
    Browse the repository at this point in the history

  9. Merge branch 'dev' into improve_rseqc_strandedness

    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    3733031 View commit details
    Browse the repository at this point in the history

  10. Merge branch 'dev' into document_fastp_sampling

    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    d4cd013 View commit details
    Browse the repository at this point in the history

  11. Merge pull request #1309 from nf-core/document_fastp_sampling 

    Document FASTP sampling
    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    f203857 View commit details
    Browse the repository at this point in the history

  12. Add existence checks

    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    7645c07 View commit details
    Browse the repository at this point in the history

  13. Merge branch 'dev' into fix_gtf_unzip

    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    191535b View commit details
    Browse the repository at this point in the history

  14. Merge branch 'dev' into improve_rseqc_strandedness

    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    231fba6 View commit details
    Browse the repository at this point in the history

  15. Merge branch 'dev' into subway_map_again

    @maxulysse
    maxulysse committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    569d2f5 View commit details
    Browse the repository at this point in the history

  16. correct order

    @maxulysse
    maxulysse committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    9640d17 View commit details
    Browse the repository at this point in the history

  17. Merge pull request #1312 from nf-core/fix_gtf_unzip 

    Fix issues with unzipping of GTF/ GFF files without absolute paths
    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    292a80c View commit details
    Browse the repository at this point in the history

  18. Merge branch 'dev' into improve_rseqc_strandedness

    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    29265f0 View commit details
    Browse the repository at this point in the history

  19. Return percentages for strandedness

    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    ac9abda View commit details
    Browse the repository at this point in the history

  20. Explicitly publish lib_format_counts

    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    3ad69a7 View commit details
    Browse the repository at this point in the history

  21. Merge pull request #1307 from maxulysse/subway_map_again 

    Clarify infer strandedness step in subway map and text
    @maxulysse
    maxulysse committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    f8a9e27 View commit details
    Browse the repository at this point in the history

  22. update docs

    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    4ce478d View commit details
    Browse the repository at this point in the history

  23. Fix typo

    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    3583d2c View commit details
    Browse the repository at this point in the history

  24. Prettier

    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    eef388e View commit details
    Browse the repository at this point in the history

  25. Fix typo 

    Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
    @pinin4fjords @maxulysse
    pinin4fjords and maxulysse committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    c95c489 View commit details
    Browse the repository at this point in the history

Commits on Jun 19, 2024

  1. Merge branch 'dev' into remove-additional-ci-triggers

    @drpatelh
    drpatelh committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    2d1ecc6 View commit details
    Browse the repository at this point in the history

  2. Merge pull request #1321 from nf-core/remove-additional-ci-triggers 

    Remove push and release triggers from CI
    @drpatelh
    drpatelh committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    485f660 View commit details
    Browse the repository at this point in the history

  3. Use Github Action to detect file changes instead of custom Python code

    @adamrtalbot
    adamrtalbot committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    89722c8 View commit details
    Browse the repository at this point in the history

  4. Update CHANGELOG.md

    @adamrtalbot
    adamrtalbot committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    b6a0720 View commit details
    Browse the repository at this point in the history

  5. Merge branch 'dev' into detect-changes-via-pre-built-gha

    @adamrtalbot
    adamrtalbot committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    923ba72 View commit details
    Browse the repository at this point in the history

  6. Merge pull request #1322 from adamrtalbot/detect-changes-via-pre-buil… 

    …t-gha

Use Github Action to detect file changes instead of custom Python code
    @adamrtalbot
    adamrtalbot committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    73fde4c View commit details
    Browse the repository at this point in the history

  7. Update actions/checkout to v4

    @adamrtalbot
    adamrtalbot committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    439ac99 View commit details
    Browse the repository at this point in the history

  8. Set maximum on bars per column

    @pinin4fjords
    pinin4fjords committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    035e85f View commit details
    Browse the repository at this point in the history

  9. Pass/fail in separate mqc column

    @pinin4fjords
    pinin4fjords committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    cdbc971 View commit details
    Browse the repository at this point in the history

  10. Merge branch 'dev' into improve_rseqc_strandedness

    @pinin4fjords
    pinin4fjords committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    0b16071 View commit details
    Browse the repository at this point in the history

  11. Merge branch 'improve_rseqc_strandedness' of github.com:nf-core/rnase… 

    …q into improve_rseqc_strandedness
    @pinin4fjords
    pinin4fjords committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    6eb5b06 View commit details
    Browse the repository at this point in the history

  12. Merge pull request #1323 from nf-core/update-actions-checkout-to-v4 

    Update actions/checkout to v4
    @drpatelh
    drpatelh committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    139f6c6 View commit details
    Browse the repository at this point in the history

  13. Fix multiqc config for cell colors to highlight strandedness

    @pinin4fjords
    pinin4fjords committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    dc22231 View commit details
    Browse the repository at this point in the history

  14. Fix strand status conditional

    @pinin4fjords
    pinin4fjords committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    bd48aa7 View commit details
    Browse the repository at this point in the history

  15. update strand check image

    @pinin4fjords
    pinin4fjords committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    36c6658 View commit details
    Browse the repository at this point in the history

  16. Fix multiqc yaml

    @pinin4fjords
    pinin4fjords committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    e45e521 View commit details
    Browse the repository at this point in the history

  17. fix up params + usage

    @pinin4fjords
    pinin4fjords committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    4dd03ca View commit details
    Browse the repository at this point in the history

  18. Merge pull request #1306 from nf-core/improve_rseqc_strandedness 

    Overhaul strandedness detection / comparison
    @pinin4fjords
    pinin4fjords committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    bd64ab6 View commit details
    Browse the repository at this point in the history

  19. Update CHANGELOG

    @drpatelh
    drpatelh committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    1029f20 View commit details
    Browse the repository at this point in the history

  20. Reorder genome reference params

    @drpatelh
    drpatelh committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    d21958b View commit details
    Browse the repository at this point in the history

  21. Fix tags in modules

    @drpatelh
    drpatelh committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    00cf111 View commit details
    Browse the repository at this point in the history

  22. Fix tags in subworkflows

    @drpatelh
    drpatelh committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    4b8e110 View commit details
    Browse the repository at this point in the history

  23. Rename pipeline level tests

    @drpatelh
    drpatelh committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    816bbde View commit details
    Browse the repository at this point in the history

  24. Update CHANGELOG with new parameters

    @drpatelh
    drpatelh committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    ce66b00 View commit details
    Browse the repository at this point in the history

  25. Change number param to have decimal place

    @drpatelh
    drpatelh committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    c7c48d8 View commit details
    Browse the repository at this point in the history

  26. Fix spacing

    @drpatelh
    drpatelh committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    1c6a944 View commit details
    Browse the repository at this point in the history

  27. Fix syntax consistency

    @drpatelh
    drpatelh committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    302e456 View commit details
    Browse the repository at this point in the history

  28. Fix prettier

    @drpatelh
    drpatelh committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    bcbfe37 View commit details
    Browse the repository at this point in the history

Commits on Jun 20, 2024

  1. Update CHANGELOG

    @drpatelh
    drpatelh committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    1cf2d14 View commit details
    Browse the repository at this point in the history

  2. Move config block back where it was

    @drpatelh
    drpatelh committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    f1ac077 View commit details
    Browse the repository at this point in the history

  3. Fix multiqc message

    @pinin4fjords
    pinin4fjords committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    634e44a View commit details
    Browse the repository at this point in the history

  4. Fix params issues

    @pinin4fjords
    pinin4fjords committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    14d27c3 View commit details
    Browse the repository at this point in the history

  5. Update mqc strand screenshot

    @pinin4fjords
    pinin4fjords committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    36617e4 View commit details
    Browse the repository at this point in the history

  6. Update CHANGELOG

    @pinin4fjords
    pinin4fjords committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    bee3d1e View commit details
    Browse the repository at this point in the history

  7. Rename pipeline level tests

    @drpatelh
    drpatelh committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    100ae0a View commit details
    Browse the repository at this point in the history

  8. Move Conda dependencies for local modules to individual environment file

    @drpatelh
    drpatelh committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    7e6827e View commit details
    Browse the repository at this point in the history

  9. Update CHANGELOG

    @drpatelh
    drpatelh committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    928a30e View commit details
    Browse the repository at this point in the history

  10. appease prettier

    @pinin4fjords
    pinin4fjords committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    4cd7037 View commit details
    Browse the repository at this point in the history

  11. Update usage

    @pinin4fjords
    pinin4fjords committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    18f59c7 View commit details
    Browse the repository at this point in the history

  12. Merge pull request #1326 from drpatelh/local_envs 

    Move Conda dependencies for local modules to individual environment file
    @drpatelh
    drpatelh committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    83e18b6 View commit details
    Browse the repository at this point in the history

  13. Merge branch 'dev' into strand_param_fixes

    @drpatelh
    drpatelh committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    b98095c View commit details
    Browse the repository at this point in the history

  14. Merge pull request #1325 from nf-core/strand_param_fixes 

    Minor fixes to strandedness settings and messaging
    @drpatelh
    drpatelh committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    6fc20bb View commit details
    Browse the repository at this point in the history

  15. Merge branch 'dev' into updates

    @drpatelh
    drpatelh committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    aae6587 View commit details
    Browse the repository at this point in the history

  16. Merge pull request #1324 from drpatelh/updates 

    Fix tags entries and rename pipeline level tests
    @drpatelh
    drpatelh committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    579684a View commit details
    Browse the repository at this point in the history

  17. Remove tags from all nf-test files

    @drpatelh
    drpatelh committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    178c45a View commit details
    Browse the repository at this point in the history

  18. Add nf-test for STAR-RSEM and HISAT2 aligners

    @adamrtalbot
    adamrtalbot committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    61c5dcc View commit details
    Browse the repository at this point in the history

  19. remove tags

    @adamrtalbot
    adamrtalbot committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    fa40d20 View commit details
    Browse the repository at this point in the history

  20. Merge branch 'dev' into alternative_aligners_nf-test

    @adamrtalbot
    adamrtalbot committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    6d29884 View commit details
    Browse the repository at this point in the history

  21. CHANGELOG

    @adamrtalbot
    adamrtalbot committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    153a9a1 View commit details
    Browse the repository at this point in the history

  22. test naming conventions

    @adamrtalbot
    adamrtalbot committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    7cda5c2 View commit details
    Browse the repository at this point in the history

  23. Update CHANGELOG

    @drpatelh
    drpatelh committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    9dbdd2c View commit details
    Browse the repository at this point in the history

  24. Update tests/hisat2.main.nf.test 

    Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
    @adamrtalbot @drpatelh
    adamrtalbot and drpatelh committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    43c709f View commit details
    Browse the repository at this point in the history

  25. Update tests/star_rsem.main.nf.test 

    Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
    @adamrtalbot @drpatelh
    adamrtalbot and drpatelh committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    3acbeb8 View commit details
    Browse the repository at this point in the history

  26. Rename files in line with other tests

    @adamrtalbot
    adamrtalbot committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    0e5cc2c View commit details
    Browse the repository at this point in the history

  27. Merge pull request #1329 from drpatelh/updates 

    Remove tags from all nf-test files
    @drpatelh
    drpatelh committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    53e59a8 View commit details
    Browse the repository at this point in the history

  28. Merge branch 'dev' into alternative_aligners_nf-test

    @drpatelh
    drpatelh committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    69faba1 View commit details
    Browse the repository at this point in the history

  29. Merge pull request #1328 from adamrtalbot/alternative_aligners_nf-test 

    Add nf-test for STAR-RSEM and HISAT2 aligners
    @drpatelh
    drpatelh committed Jun 20, 2024
    Configuration menu
    Copy the full SHA
    c5b4fee View commit details
    Browse the repository at this point in the history