From d6041289e3d82cf7e2c8bd132fd89a1384b7b110 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 22 May 2024 09:03:16 +0100 Subject: [PATCH 1/5] Update differentialabundance_report.Rmd --- assets/differentialabundance_report.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd index 7bf41c12..861f55e0 100644 --- a/assets/differentialabundance_report.Rmd +++ b/assets/differentialabundance_report.Rmd @@ -510,7 +510,7 @@ contrasts_to_print$model <- sapply(contrasts_to_print$Id, function(id) { } }) -print( htmltools::tagList(datatable(contrasts_to_print, caption = paste0("Table of contrasts"), rownames = FALSE, options = list(dom = 't')) )) +print( htmltools::tagList(datatable(contrasts_to_print, caption = paste0("Table of contrasts"), rownames = FALSE, options = list(dom = ifelse(nrow(contrasts_to_print) > 10, 'tp', 't'))) )) ``` # Results From 20a44d626e08553ae9c1c9fc59088fd0bed23cf3 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 22 May 2024 09:06:36 +0100 Subject: [PATCH 2/5] Update CHANGELOG.md --- CHANGELOG.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3d844a1e..8c24f8d6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,16 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v1.6.0dev - xxxx-xx-xx + +### Added + +### Fixed + +- [[#272](https://github.com/nf-core/differentialabundance/pull/272)] - Show >10 contrasts in report ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO)) + +### Changed + ## v1.5.0 ### `Added` From c05522a34bb4b081f2cb824979f3dcfabec5a4e8 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 22 May 2024 09:08:02 +0100 Subject: [PATCH 3/5] Update CHANGELOG.md --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8c24f8d6..c5825d81 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.6.0dev - xxxx-xx-xx +## v1.6.0dev - 2024-05-08 ### Added @@ -13,7 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed -## v1.5.0 +## v1.5.0 - 2024-11-27 ### `Added` From ab26e4c9f9543b58d18bc8758300f45e39ecb31d Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 22 May 2024 12:08:41 +0100 Subject: [PATCH 4/5] fix files_unchanged --- .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/linting.yml | 19 +++++++++---------- .github/workflows/linting_comment.yml | 2 +- 3 files changed, 11 insertions(+), 12 deletions(-) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 70d62a73..89778df2 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/diff - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/differentialabundance/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/differentialabundance _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 (`nf-test test main.nf.test -profile test,docker`). +- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 073e1876..1fcafe88 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -14,13 +14,12 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - - name: Set up Python 3.11 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - name: Set up Python 3.12 + uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: - python-version: 3.11 - cache: "pip" + python-version: "3.12" - name: Install pre-commit run: pip install pre-commit @@ -32,14 +31,14 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: - python-version: "3.11" + python-version: "3.12" architecture: "x64" - name: Install dependencies @@ -60,7 +59,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 + uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index b706875f..40acc23f 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3 + uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3 with: workflow: linting.yml workflow_conclusion: completed From bcfde263d117382137b6f4fe515b5817d9a1fc5e Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 22 May 2024 13:22:02 +0100 Subject: [PATCH 5/5] Update CHANGELOG.md --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 49e93d17..2325f46c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.6.0dev - 2024-05-08 +## v1.6.0dev - xxxx-xx-xx ### Added @@ -13,7 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed -## v1.5.0 - 2024-11-27 +## v1.5.0 - 2024-05-08 ### `Added`