Merge pull request #185 from nf-core/dev

Dev -> master for v1.3.1
nf-core · Oct 27, 2023 · 44c449b · 44c449b
2 parents e2e2676 + 33e4234
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,15 +3,27 @@
 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).
 
-## v1.3.0 - 2023-10-25
+## v1.3.1 - 2023-10-26
+
+### `Added`
+
+### `Fixed`
+
+- [[#183](https://github.com/nf-core/differentialabundance/pull/183)] - Fix logging for dendrograms ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
+
+### `Changed`
+
+- [[#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 - 2023-10-24
 
 ### `Added`
 
 - [[#124](https://github.com/nf-core/differentialabundance/pull/124)] - Template update for nf-core/tools v2.8 ([@pinin4fjords](https://github.com/pinin4fjords), review by [@jasmezz](https://github.com/jasmezz))
 - [[#129](https://github.com/nf-core/differentialabundance/pull/129)] - Module updates to fit with recent registry changes ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse), [@adamrtalbot](https://github.com/adamrtalbot))
 - [[#130](https://github.com/nf-core/differentialabundance/pull/130)] - Document reasons for lack of differential expression ([@pinin4fjords](https://github.com/pinin4fjords), review by [@jfy133](https://github.com/jfy133))
 - [[#131](https://github.com/nf-core/differentialabundance/pull/131)] - Improve gtf to table configurability ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
-- [# 136](https://github.com/nf-core/differentialabundance/pull/136)] - Added support for non-Affymetrix arrays via automatic download of SOFT matrices in GEO ([@azedinez](https://github.com/azedinez), review by [@pinin4fjords](https://github.com/pinin4fjords))
+- [[#136](https://github.com/nf-core/differentialabundance/pull/136)] - Added support for non-Affymetrix arrays via automatic download of SOFT matrices in GEO ([@azedinez](https://github.com/azedinez), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#137](https://github.com/nf-core/differentialabundance/pull/137)] - Add `--sizefactors_from_controls` and `--gene_id_col` for DESeq2 module to modules.config ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#145](https://github.com/nf-core/differentialabundance/pull/145)] - Template update for nf-core/tools v2.9 ([@nf-core-bot](https://github.com/nf-core-bot), review by [@pinin4fjords](https://github.com/pinin4fjords), [@WackerO](https://github.com/WackerO))
 - [[#147](https://github.com/nf-core/differentialabundance/pull/147)] - Add Maxquant analysis module ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))

diff --git a/README.md b/README.md
@@ -100,7 +100,7 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/differentialabundance was originally written by Jonathan Manning ([@pinin4fjords](https://github.com/pinin4fjords)) and Oskar Wacker ([@WackerO](https://github.com/WackerO)). Jonathan Manning is an employee of Healx, an AI-powered, patient-inspired tech company, accelerating the discovery and development of treatments for rare diseases. We are grateful for their support of open science in this project.
+nf-core/differentialabundance was originally written by Jonathan Manning ([@pinin4fjords](https://github.com/pinin4fjords)) and Oskar Wacker ([@WackerO](https://github.com/WackerO)). Jonathan Manning (now at Seqera) initially worked on this workflow as an employee of Healx, an AI-powered, patient-inspired tech company, accelerating the discovery and development of treatments for rare diseases. We are grateful for their support of open science in this project.
 
 We thank the many members of the nf-core community who assisted with this pipeline, often by reviewing module pull requests including but not limited to:
 

diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd
@@ -254,10 +254,10 @@ assay_data <- lapply(assay_files, function(x) {
 })
 
 if (!is.null(params$features_log2_assays)) {
-  # Remove brackets from assay list. TODO: Remove if this is added to cond_log2_transform_assays
-  features_log2_assays <- gsub('\\]$', '', gsub('^\\[', '', params$features_log2_assays))
-  assay_data <- cond_log2_transform_assays(assay_data, features_log2_assays)
+  # Remove brackets from assay list. TODO: remove if this is added to cond_log2_transform_assays
+  params$features_log2_assays <- gsub('\\]$', '', gsub('^\\[', '', params$features_log2_assays))
 }
+assay_data <- cond_log2_transform_assays(assay_data, params$features_log2_assays)
 
 # Now we can rename the observations rows using the title field
 rownames(observations) <- observations[[params$observations_name_col]]

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/1.3.0" 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/1.3.0/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": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5",
+                        "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/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
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