Dev -> Master for 3.13.0 release #1113
Commits on Jun 14, 2023
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Display a warning when '--star_extra_alignment_args' are used in comb…
…ination with the STAR-RSEM route.
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Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Commits on Jun 15, 2023
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Merge pull request #1049 from MatthiasZepper/ExtraStarAlignArgsWarning
Display a warning when '--star_extra_alignment_args' are used with RSEM
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Merge pull request #1048 from nf-core/maxulysse-patch-1
Update public_aws_ecr.config
Commits on Jun 21, 2023
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Merge pull request #1051 from adamrtalbot/remove_public_aws_ecr_profile
Remove public_aws_ecr profile
Commits on Jun 30, 2023
Commits on Jul 5, 2023
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Merge pull request #1053 from nf-core/nf-core-template-merge-2.9
Important! Template update for nf-core/tools v2.9
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Commits on Jul 6, 2023
Commits on Jul 10, 2023
Commits on Jul 11, 2023
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Merge pull request #1057 from nf-core/subway-credits
Update credits for subway map
Commits on Jul 12, 2023
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Merge pull request #1058 from drpatelh/updates
Use nf-validation plugin for parameter and samplesheet validation
Commits on Jul 14, 2023
Commits on Jul 19, 2023
Commits on Aug 2, 2023
Commits on Aug 8, 2023
Commits on Aug 16, 2023
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Merge pull request #1060 from smoe/patch-1
README.md: Added ref to downstream analyses
Commits on Aug 30, 2023
Commits on Sep 4, 2023
Commits on Sep 5, 2023
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Revert "Actually, let's make non-use of iGenomes the default"
This reverts commit c4e17a6.
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Revert "Restore default igenomes behaviour for testing"
This reverts commit 7b063e3.
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Commits on Sep 26, 2023
Commits on Oct 5, 2023
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Reorganises local modules into subfolder/main.nf
Changes: - Moves every local module into a named subfolder - Each module uses a main.nf file - Improves consistency between modules (local and nf-core) - Should make it easier to create nf-tests Fixes #1080 - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnaseq/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/rnaseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir \u003cOUTDIR\u003e`). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. - [ ] `CHANGELOG.md` is updated. - [ ] `README.md` is updated (including new tool citations and authors/contributors).
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- Moves every local subworkflow into a named subfolder - Each workflow uses a main.nf file - Improves consistency between subworkflows (local and nf-core) - Should make it easier to create nf-tests
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Commits on Oct 9, 2023
Commits on Oct 10, 2023
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Reorganise arguments for clearer syntax
Changes: - Grouped arguments into sections based on _what they do_ - Reordered slightly to go in chronological order of the pipeline and set up - I think it's clearer for a new user Fixes #1090
Commits on Oct 11, 2023
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Merge pull request #1088 from nf-core/2.10_documentation_template_upd…
…ates Update the CODE_OF_CONDUCT and CONTRIBUTING with nf-core template 2.10
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Merge pull request #1091 from adamrtalbot/1090_tidy_cli_args
Reorganise arguments for clearer syntax
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Merge pull request #1083 from nf-core/reorg_local_modules_to_subfolders
Reorganise local modules into subfolder/main.nf for consistency
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Commits on Oct 12, 2023
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Merge pull request #1078 from nf-core/nf-core-template-merge-2.10
Important! Template update for nf-core/tools v2.10
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Commits on Oct 13, 2023
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Merge pull request #1073 from nf-core/igenomes_warning
Update usage.md for igenomes warning
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Merge pull request #1093 from drpatelh/fixes
Update all nf-core/modules in pipeline
Commits on Oct 31, 2023
Commits on Nov 2, 2023
Commits on Nov 3, 2023
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Merge branch 'kallisto_quant' of https://github.com/nf-core/rnaseq in…
…to kallisto_quant
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Commits on Nov 6, 2023
Commits on Nov 7, 2023
Commits on Nov 8, 2023
Commits on Nov 9, 2023
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[skip ci] Update config per latest
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
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Commits on Nov 10, 2023
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Merge pull request #1108 from maxulysse/config_update
update config to enable usage of a custom config
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Commits on Nov 13, 2023
Commits on Nov 14, 2023
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[skip ci] Apply suggestions from code review
Co-authored-by: Matthias Zepper <6963520+MatthiasZepper@users.noreply.github.com>
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Commits on Nov 15, 2023
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Merge pull request #1106 from nf-core/kallisto_quant
Kallisto quantification
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Merge pull request #1107 from nf-core/stringtie_gtf
Expand GTF filtering to remove rows with empty transcript ID when required, fix STAR GTF usage
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Commits on Nov 16, 2023
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Merge pull request #1114 from nf-core/skip-ci]-update_contribs
Pre-release fixes for 3.13.0
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Merge pull request #1116 from nf-core/maxime_feedback
Maxime feedback
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Merge pull request #1117 from maxulysse/subway_map
FIX: Subway map
Commits on Nov 17, 2023
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Merge pull request #1120 from maxulysse/subway_map
final updates on subway map