Merge pull request #91 from nf-core/dev

Dev -> master for v1.1.1
nf-core · Mar 3, 2023 · 47e3d92 · 47e3d92
2 parents c5de056 + 4d59606
commit 47e3d92
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,12 @@
 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).
 
+## v1.1.1 - 2023-03-02
+
+### `Fixed`
+
+- [[#89](https://github.com/nf-core/differentialabundance/pull/89)] - Sanitise for differential ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
+
 ## v1.1.0 - 2023-02-22
 
 ### `Added`
@@ -13,13 +19,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
-- [[#55](https://github.com/nf-core/differentialabundance/pull/55)] - Don't drop dimensions in report with single informative variable ([@pinin4fjords](https://github.com/pinin4fjords), reviewed by [@mashehu](https://github.com/mashehu))
+- [[#55](https://github.com/nf-core/differentialabundance/pull/55)] - Don't drop dimensions in report with single informative variable ([@pinin4fjords](https://github.com/pinin4fjords), review by [@mashehu](https://github.com/mashehu))
 - [[#57](https://github.com/nf-core/differentialabundance/issues/57)] - Update module shinyngs/validatefomcomponents and bump other shinyngs modules to resolve [[#56](https://github.com/nf-core/differentialabundance/issues/56)] ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
-- [[#65](https://github.com/nf-core/differentialabundance/pull/65)] - Update shinyngs modules to latest to resolve palette issues reported by [@Shellfishgene](https://github.com/Shellfishgene) ([@pinin4fjords](https://github.com/pinin4fjords), reviewed by [@mashehu](https://github.com/mashehu))
+- [[#65](https://github.com/nf-core/differentialabundance/pull/65)] - Update shinyngs modules to latest to resolve palette issues reported by [@Shellfishgene](https://github.com/Shellfishgene) ([@pinin4fjords](https://github.com/pinin4fjords), review by [@mashehu](https://github.com/mashehu))
 - [[#67](https://github.com/nf-core/differentialabundance/issues/67)] - Error when contrast is blocking by multiple variables ([@pinin4fjords](https://github.com/pinin4fjords), reported by [@clstacy](https://github.com/clstacy), review by [@jfy133](https://github.com/jfy133))
 - [[#71](https://github.com/nf-core/differentialabundance/pull/71)] - Add palette options, bring full check.names fixes from upstream, closing [[#68](https://github.com/nf-core/differentialabundance/issues/68)] reported by [@Shellfishgene](https://github.com/Shellfishgene), [[#69](https://github.com/nf-core/differentialabundance/issues/69)] reported by [@clstacy](https://github.com/clstacy). ([@pinin4fjords](https://github.com/pinin4fjords), reported by [@clstacy](https://github.com/clstacy), review by [@matthdsm](https://github.com/matthdsm), [@WackerO](https://github.com/WackerO))
 - [[#73](https://github.com/nf-core/differentialabundance/pull/73)] - Make `--matrix`, `--input`, `--features` accept either CSV,TXT or TSV files as input ([@apeltzer](https://github.com/apeltzer), review by [@pinin4fjords](https://github.com/pinin4fjords))
-- [[#75](https://github.com/nf-core/differentialabundance/pull/75)] - Bump deseq2/differential for check.names fix ([@pinin4fjords](https://github.com/pinin4fjords), reviewed by [@apeltzer](https://github.com/apeltzer))
+- [[#75](https://github.com/nf-core/differentialabundance/pull/75)] - Bump deseq2/differential for check.names fix ([@pinin4fjords](https://github.com/pinin4fjords), review by [@apeltzer](https://github.com/apeltzer))
 - [[#76](https://github.com/nf-core/differentialabundance/pull/76)] - Fix up non-gtf operation using matrix as annotation source ([@pinin4fjords](https://github.com/pinin4fjords), reported by [@apeltzer](https://github.com/apeltzer), review by [@apeltzer](https://github.com/apeltzer))
 - [[#82](https://github.com/nf-core/differentialabundance/pull/82)] - Address v1.1.0 pre-release feedback (subway map fixes) ([@pinin4fjords](https://github.com/pinin4fjords), reported by [@mashehu](https://github.com/mashehu))
 

diff --git a/modules.json b/modules.json
@@ -37,7 +37,7 @@
                     },
                     "deseq2/differential": {
                         "branch": "master",
-                        "git_sha": "2d2e936e5a0bdb2888112e2d2220eb0895d486e1",
+                        "git_sha": "dbffa8da6e9f065a5b7240255c51cbd839f5df43",
                         "installed_by": ["modules"]
                     },
                     "gsea/gsea": {
@@ -52,7 +52,7 @@
                     },
                     "limma/differential": {
                         "branch": "master",
-                        "git_sha": "960cc23c7bb97ff718e162efeefdd842fa8f5c70",
+                        "git_sha": "dbffa8da6e9f065a5b7240255c51cbd839f5df43",
                         "installed_by": ["modules"]
                     },
                     "rmarkdownnotebook": {

diff --git a/modules/nf-core/deseq2/differential/templates/deseq_de.R b/modules/nf-core/deseq2/differential/templates/deseq_de.R
diff --git a/modules/nf-core/limma/differential/templates/limma_de.R b/modules/nf-core/limma/differential/templates/limma_de.R
diff --git a/nextflow.config b/nextflow.config
@@ -313,7 +313,7 @@ manifest {
     description     = 'Differential abundance analysis'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '1.1.0'
+    version         = '1.1.1'
     doi             = '10.5281/zenodo.7568000'
 }