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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>
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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
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Commits on Jun 20, 2023
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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
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Commits on Jun 30, 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
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Commits on Jul 10, 2023
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Commits on Jul 11, 2023
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Merge pull request #1057 from nf-core/subway-credits
Update credits for subway map
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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
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Commits on Jul 14, 2023
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Commits on Aug 16, 2023
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Merge pull request #1060 from smoe/patch-1
README.md: Added ref to downstream analyses
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Commits on Aug 30, 2023
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Commits on Sep 4, 2023
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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
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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
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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
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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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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
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Merge branch 'kallisto_quant' of https://github.com/nf-core/rnaseq in…
…to kallisto_quant
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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
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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
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Commits on Nov 17, 2023
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Merge pull request #1120 from maxulysse/subway_map
final updates on subway map
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