The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
- #61 - Update Metro Map (@maxulysse, reviewed by @drpatelh)
- #71 - Template update for nf-core/tools v3.0.2 (@nf-corebot, (@maxulysse, reviewed by @JackCurragh), @FelixKrueger)
- #73 - Pipeline level snapshots with nf-test ((@maxulysse, reviewed by @pinin4fjords))
- #77 - Update
RIBOTRICER_PREPAREORFSto increase resource allocation (@iraiosub) - #83 - Fix skip_ribotish (@pinin4fjords, reviewed by @FelixKrueger)
- #85 - Rationalise sorted bam/bai publishing (@pinin4fjords, reviewed by @FelixKrueger)
- #86 - Important! Template update for nf-core/tools v3.2.0 (@nf-core-bot, review by @pinin4fjords)
- #87 - Bump versions pre-release to 1.1.0 (@pinin4fjords, reviewed by @FelixKrueger)
- #92 - Bump anota2seq for ordering fix (@pinin4fjords, reviewed by @FelixKrueger)
- #93 - Bump anota2seq for dollar fix (@pinin4fjords, reviewed by @FelixKrueger)
- #94 - Fix value channel for multi-contrast case (@pinin4fjords, reviewed by @FelixKrueger)
- #96 - Fix minor linting issue for release (@pinin4fjords, reviewed by @FelixKrueger)
- #97 - Remove the on_pull_request_target trigger from the download test (@pinin4fjords)
- #98 - Bump gunzip due to release CI failure (@pinin4fjords)
- #99 - Remove conda from release CI (@pinin4fjords)
- #100 - Fix gunzip in snapshot (@pinin4fjords)
- #60 - Pass empty value to samtools sort in UMI handling branch (@JackCurragh, reviewed by @FelixKrueger, @maxulysse)
- #61 - Update subworkflow
utils_nfcore_pipeline(@maxulysse, reviewed by @drpatelh) - #75 - UMI fixes: solve deduplication issue and update input handling for Salmon (@iraiosub, reviewed by @FelixKrueger, @pinin4fjords)
- #79 - Move UMI handling to subworkflow, update modules and subworkflows, deal with docs and config fallout (@pinin4fjords, reviewed by @FelixKrueger)
- #90 - --subset_to_contrast_samples must be true for anota2seq (@pinin4fjords, reviewed by @FelixKrueger)
| Dependency | Old version | New version |
|---|---|---|
MultiQC |
1.21 | 1.25.1 |
| Old parameter | New parameter |
|---|---|
--help_full |
|
--show_hidden |
|
--skip_linting |
|
--extra_fqlint_args |
|
--umi_dedup_tool |
|
--validationFailUnrecognisedParams |
|
--validationLenientMode |
|
--validationSchemaIgnoreParams |
|
--validationShowHiddenParams |
- #53 - Bump to v1.0.1 and set Zenodo (@pinin4fjords, review by @maxulysse)
- #54 - Add legal logos and first metro map (@FelixKrueger, review by @maxulysse)
- #57 - Minor spacing changes to logo svg (@JackCurragh, reviewed by @FelixKrueger)
Initial release of nf-core/riboseq, created with the nf-core template.
- #3 - Re-initialise base template (@maxulysse, review by @pinin4fjords)
- #4 - Initialise testing an base template functionality (@pinin4fjords, review by @maxulysse)
- #8 - Preprocessing from rnaseq (@pinin4fjords, review by @maxulysse review by @adamrtalbot)
- #10 - Take preprocessing from nf-core (@pinin4fjords, review by @adamrtalbot)
- #12 - Add alignment via STAR + postprocessing ((@pinin4fjords, review by @maxulysse)
- #35 - Sortmerna: index once (@pinin4fjords, review by @maxulysse)
- #40 - Ribotricer orf prediction (@pinin4fjords, review by @maxulysse)
- #42 - Add alignment based quantification with Salmon (@pinin4fjords, review by @maxulysse)
- #43 - Add translational efficiency analysis with anota2seq (@pinin4fjords, review by @maxulysse)
- #9 - Important! Template update for nf-core/tools v2.12 (nf-core-bot, review by @pinin4fjords)
- #32 - Nf core template merge 2.13 (manual) (@pinin4fjords, review by @maxulysse, @adamrtalbot)
- #38 - Important! Template update for nf-core/tools v2.13.1 (@nf-core-bot, @pinin4fjords)
- #46 - Prerelease changes v1.0.0 (@pinin4fjords, review by @FelixKrueger)
- #51 - Change to custom logo (@JackCurragh, review by @FelixKrueger)
- #5 - Fix linting (@maxulysse, review by @pinin4fjords)
- #34 - Fix order of preprocessing steps (@pinin4fjords, review by @maxulysse)
- #36 - Bump bbsplit module to prevent index overwrites (@pinin4fjords, review by @maxulysse)
- #44 - Fix lack of fastqc in multiqc report (@pinin4fjords, review by @mashehu)
- #45 - Update CI from rnaseq, strip unused rnaseq components (@pinin4fjords, review by @jfy133)
- #48 - Remove stub option from download in CI (@pinin4fjords, review by @maxulysse)
- #49 - Fix CI (@pinin4fjords, review by @adamrtalbot)
- #50 - V1.0.0 release review fixes (@pinin4fjords, review by @maxulysse)