From 9fc9a3515cd735cac228a44b9e80b9d563d17a5a Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 4 Sep 2024 09:59:50 +0100 Subject: [PATCH 1/3] Apply Maxime's suggestions to changelog --- CHANGELOG.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2494ba6db..b9f69044a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -25,6 +25,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements ### Enhancements & fixes +- [PR #1180](https://github.com/nf-core/rnaseq/pull/1180) - Bump pipeline version to 3.15.0dev - [PR #1186](https://github.com/nf-core/rnaseq/pull/1186) - Properly update qualimap/rnaseq module (ie not patch) - [PR #1197](https://github.com/nf-core/rnaseq/pull/1197) - Delete lib directory and replace with utils\_\* subworkflows - [PR #1199](https://github.com/nf-core/rnaseq/pull/1199) - Replace modules.config with more modular config files per module/subworkflow/workflow @@ -75,7 +76,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1272](https://github.com/nf-core/rnaseq/pull/1272) - Simple pipeline level nf-tests - [PR #1274](https://github.com/nf-core/rnaseq/pull/1274) - Update bam_markduplicates_picard subworkflow - [PR #1278](https://github.com/nf-core/rnaseq/pull/1278) - Delocalise pseudo quant workflow -- [PR #1279](https://github.com/nf-core/rnaseq/pull/1279) - Add psueudoaligner pipeline level tests to test suite +- [PR #1279](https://github.com/nf-core/rnaseq/pull/1279) - Add pseudoaligner pipeline level tests to test suite - [PR #1280](https://github.com/nf-core/rnaseq/pull/1280) - Reorganise pipeline level tests into flat directory structure - [PR #1282](https://github.com/nf-core/rnaseq/pull/1282) - Fix CHANGELOG error - [PR #1283](https://github.com/nf-core/rnaseq/pull/1283) - Add output files to nf-test snapshot @@ -104,14 +105,14 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1331](https://github.com/nf-core/rnaseq/pull/1331) - Adding stubs for local modules - [PR #1334](https://github.com/nf-core/rnaseq/pull/1334) - Update all nf-core/modules and subworkflows with stubs - [PR #1335](https://github.com/nf-core/rnaseq/pull/1335) - Adding stubs at all levels -- [PR #1336](https://github.com/nf-core/rnaseq/pull/1334) - Use nf-core/setup-nf-test to install nf-test from cache during CI/CD +- [PR #1336](https://github.com/nf-core/rnaseq/pull/1336) - Use nf-core/setup-nf-test to install nf-test from cache during CI/CD - [PR #1340](https://github.com/nf-core/rnaseq/pull/1340) - Remove out-of-date Azure specific guidance - [PR #1341](https://github.com/nf-core/rnaseq/pull/1341) - Add rename in the MultiQC report for samples without techreps - [PR #1342](https://github.com/nf-core/rnaseq/pull/1342) - Factor out preprocessing - [PR #1345](https://github.com/nf-core/rnaseq/pull/1345) - Fix preprocessing call - [PR #1350](https://github.com/nf-core/rnaseq/pull/1350) - Reduce resource usage for sort process in bedtools/genomecov -- [PR #1353](https://github.com/nf-core/rnaseq/pull/1353) - Correct conditional for salmon indexing in preprocessing workflow - [PR #1352](https://github.com/nf-core/rnaseq/pull/1352) - Assorted fixes to MultiQC usage +- [PR #1353](https://github.com/nf-core/rnaseq/pull/1353) - Correct conditional for salmon indexing in preprocessing workflow - [PR #1355](https://github.com/nf-core/rnaseq/pull/1355) - Make all curves on subway map better looking, and all lines now have the same width - [PR #1357](https://github.com/nf-core/rnaseq/pull/1357) - Fix anchor issue in multiqc - [PR #1358](https://github.com/nf-core/rnaseq/pull/1358) - Update test profiles to restore a static URI for megatests From 90a1e838cc98fd7558f18cb2dd106e9589d1660d Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 4 Sep 2024 10:03:12 +0100 Subject: [PATCH 2/3] Add new PRs to changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index b9f69044a..c5505b5cc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -124,6 +124,8 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1363](https://github.com/nf-core/rnaseq/pull/1363) - Update dupradar script - [PR #1366](https://github.com/nf-core/rnaseq/pull/1366) - Clarify docs on different tximport count files - [PR #1367](https://github.com/nf-core/rnaseq/pull/1367) - Clarify design formula and blind dispersion estimation +- [PR #1370](https://github.com/nf-core/rnaseq/pull/1370) - Bump versions for 3.15.0 +- [PR #1371](https://github.com/nf-core/rnaseq/pull/1371) - Apply Maxime's changelog edits ### Parameters From 2b32127a1d9641d22b69e63fbe92045c4f6b5b36 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 4 Sep 2024 10:06:56 +0100 Subject: [PATCH 3/3] Bump CI --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c5505b5cc..23eb1fe16 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -125,7 +125,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1366](https://github.com/nf-core/rnaseq/pull/1366) - Clarify docs on different tximport count files - [PR #1367](https://github.com/nf-core/rnaseq/pull/1367) - Clarify design formula and blind dispersion estimation - [PR #1370](https://github.com/nf-core/rnaseq/pull/1370) - Bump versions for 3.15.0 -- [PR #1371](https://github.com/nf-core/rnaseq/pull/1371) - Apply Maxime's changelog edits +- [PR #1371](https://github.com/nf-core/rnaseq/pull/1371) - Apply Maxime's CHANGELOG edits ### Parameters