Merge pull request #184 from nf-core/release_v1.3.1

Release v1.3.1
nf-core · Oct 26, 2023 · 33e4234 · 33e4234
2 parents 8f1be52 + b7e7528
commit 33e4234
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diff --git 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).
 
-## v1.4.0dev
+## v1.3.1 - 2023-10-26
 
 ### `Added`
 
@@ -15,7 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [[#182](https://github.com/nf-core/differentialabundance/pull/182)] - Fixed Jon's employer ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
 
-## v1.3.0 - 2023-10-25
+## v1.3.0 - 2023-10-24
 
 ### `Added`
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/differentialabundance/releases/tag/dev" target="_blank">nf-core/differentialabundance</a>
+  This report has been generated by the <a href="https://github.com/nf-core/differentialabundance/releases/tag/1.3.1" target="_blank">nf-core/differentialabundance</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/differentialabundance/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/differentialabundance/1.3.1/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-differentialabundance-methods-description":
     order: -1000

diff --git a/modules.json b/modules.json
@@ -7,97 +7,97 @@
                 "nf-core": {
                     "affy/justrma": {
                         "branch": "master",
-                        "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
+                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
                         "installed_by": ["modules"]
                     },
                     "atlasgeneannotationmanipulation/gtf2featureannotation": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
                         "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
                         "installed_by": ["modules"]
                     },
                     "custom/matrixfilter": {
                         "branch": "master",
-                        "git_sha": "e432a05dc59832d55307442264ad2b70039f5e3a",
+                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
                         "installed_by": ["modules"]
                     },
                     "custom/tabulartogseacls": {
                         "branch": "master",
-                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
+                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
                         "installed_by": ["modules"]
                     },
                     "custom/tabulartogseagct": {
                         "branch": "master",
-                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
+                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
                         "installed_by": ["modules"]
                     },
                     "deseq2/differential": {
                         "branch": "master",
-                        "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
+                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
                         "installed_by": ["modules"]
                     },
                     "geoquery/getgeo": {
                         "branch": "master",
-                        "git_sha": "6814b0659c51e447684a58c2b834a9f3b530540d",
+                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
                         "installed_by": ["modules"]
                     },
                     "gsea/gsea": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "8663c9d215573d4bd0417c93dbc310aa9e6720a4",
+                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
                         "installed_by": ["modules"]
                     },
                     "limma/differential": {
                         "branch": "master",
-                        "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
+                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
                         "installed_by": ["modules"]
                     },
                     "proteus/readproteingroups": {
                         "branch": "master",
-                        "git_sha": "685765c4a5e3423d20f74aa9c4405ef0b8c4748d",
+                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
                         "installed_by": ["modules"]
                     },
                     "rmarkdownnotebook": {
                         "branch": "master",
-                        "git_sha": "4e640839b1076da7c2a2a4a8f160815e00eedfba",
+                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/app": {
                         "branch": "master",
-                        "git_sha": "1b2fa2138849ac09b3d5c1e25ed70650ec1ebd7b",
+                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/staticdifferential": {
                         "branch": "master",
-                        "git_sha": "1b2fa2138849ac09b3d5c1e25ed70650ec1ebd7b",
+                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/staticexploratory": {
                         "branch": "master",
-                        "git_sha": "1b2fa2138849ac09b3d5c1e25ed70650ec1ebd7b",
+                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/validatefomcomponents": {
                         "branch": "master",
-                        "git_sha": "1b2fa2138849ac09b3d5c1e25ed70650ec1ebd7b",
+                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
                         "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
+                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
                         "installed_by": ["modules"]
                     },
                     "zip": {
                         "branch": "master",
-                        "git_sha": "9ba4f5972ae27474f752ddb20e855f48047aa6c8",
+                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/nf-core/affy/justrma/environment.yml b/modules/nf-core/affy/justrma/environment.yml
diff --git a/modules/nf-core/affy/justrma/main.nf b/modules/nf-core/affy/justrma/main.nf
diff --git a/modules/nf-core/affy/justrma/meta.yml b/modules/nf-core/affy/justrma/meta.yml
diff --git a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml
diff --git a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf
diff --git a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml
diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
diff --git a/modules/nf-core/custom/matrixfilter/environment.yml b/modules/nf-core/custom/matrixfilter/environment.yml
diff --git a/modules/nf-core/custom/matrixfilter/main.nf b/modules/nf-core/custom/matrixfilter/main.nf
diff --git a/modules/nf-core/custom/matrixfilter/meta.yml b/modules/nf-core/custom/matrixfilter/meta.yml
diff --git a/modules/nf-core/custom/tabulartogseacls/environment.yml b/modules/nf-core/custom/tabulartogseacls/environment.yml
diff --git a/modules/nf-core/custom/tabulartogseacls/main.nf b/modules/nf-core/custom/tabulartogseacls/main.nf
diff --git a/modules/nf-core/custom/tabulartogseacls/meta.yml b/modules/nf-core/custom/tabulartogseacls/meta.yml
diff --git a/modules/nf-core/custom/tabulartogseagct/environment.yml b/modules/nf-core/custom/tabulartogseagct/environment.yml
diff --git a/modules/nf-core/custom/tabulartogseagct/main.nf b/modules/nf-core/custom/tabulartogseagct/main.nf
diff --git a/modules/nf-core/custom/tabulartogseagct/meta.yml b/modules/nf-core/custom/tabulartogseagct/meta.yml
diff --git a/modules/nf-core/deseq2/differential/environment.yml b/modules/nf-core/deseq2/differential/environment.yml
diff --git a/modules/nf-core/deseq2/differential/main.nf b/modules/nf-core/deseq2/differential/main.nf