Merge pull request #374 from nf-core/modules_update

Updated all nf-core modules and subworkflows
nf-core · Dec 5, 2024 · 9a84f4b · 9a84f4b
2 parents 6307b48 + 2af5439
commit 9a84f4b
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -36,7 +36,7 @@ jobs:
       matrix:
         NXF_VER:
           - "24.04.2"
-          - "latest-everything"
+          - "latest-stable"
         test_profile:
           - "test"
           - "nogtf"

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,10 +8,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 
 - [[#358](https://github.com/nf-core/differentialabundance/pull/358)] - Added software version check in nf-tests and gene biotype column check in `.Rmd` ([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords))
+- [[#354](https://github.com/nf-core/differentialabundance/pull/354)] - Warning message within the R Markdown report to control when genes don't have annotation data ([@alanmmobbs93](https://github.com/alanmmobbs93)). Review by [@WackerO](https://github.com/WackerO) and [@pinin4fjords](https://github.com/pinin4fjords).
 - [[#345](https://github.com/nf-core/differentialabundance/pull/345)] - Plot differentially expressed genes by gene biotype ([@atrigila](https://github.com/atrigila), review by [@grst](https://github.com/grst))
 - [[#343](https://github.com/nf-core/differentialabundance/pull/343)] - Add pipeline-level nf-tests ([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords) and [@nschcolnicov](https://github.com/nschcolnicov))
 - [[#286](https://github.com/nf-core/differentialabundance/pull/286)] - Integration of limma voom for rnaseq data ([@KamilMaliszArdigen](https://github.com/KamilMaliszArdigen), review by [@pinin4fjords](https://github.com/pinin4fjords))
-- [[#354](https://github.com/nf-core/differentialabundance/pull/354)] - Warning message within the R Markdown report to control when genes don't have annotation data ([@alanmmobbs93](https://github.com/alanmmobbs93)). Review by [@WackerO](https://github.com/WackerO) and [@pinin4fjords](https://github.com/pinin4fjords).
 
 ### Fixed
 
@@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+- [[#374](https://github.com/nf-core/differentialabundance/pull/374)] - Update all modules and subworkflows ([@nschcolnicov](https://github.com/nschcolnicov), review by [@pinin4fjords](https://github.com/pinin4fjords)).
 - [[#348](https://github.com/nf-core/differentialabundance/pull/348)] - Update test_full profile matrix file and indentation of profiles in nextflow.config ([@nschcolnicov](https://github.com/nschcolnicov), review by [@WackerO](https://github.com/WackerO) and [@pinin4fjords](https://github.com/pinin4fjords))
 
 ## v1.5.0 - 2024-05-08

diff --git a/conf/test.config b/conf/test.config
@@ -10,14 +10,6 @@
 ----------------------------------------------------------------------------------------
 */
 
-process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '15.GB',
-        time: '1.h'
-    ]
-}
-
 params {
     study_name = 'SRP254919'
     config_profile_name        = 'Test profile'

diff --git a/conf/test_affy.config b/conf/test_affy.config
@@ -18,11 +18,6 @@ params {
     config_profile_name        = 'Affy array test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/testdata/GSE50790.csv'
     contrasts = 'https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/testdata/GSE50790_contrasts.csv'

diff --git a/conf/test_maxquant.config b/conf/test_maxquant.config
@@ -18,11 +18,6 @@ params {
     config_profile_name        = 'MaxQuant test profile'
     config_profile_description = 'MaxQuant test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     input     = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/proteomics/maxquant/MaxQuant_samplesheet.tsv'
     matrix    = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/proteomics/maxquant/MaxQuant_proteinGroups.txt'

diff --git a/conf/test_nogtf.config b/conf/test_nogtf.config
@@ -18,11 +18,6 @@ params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
 
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv'

diff --git a/conf/test_soft.config b/conf/test_soft.config
@@ -18,11 +18,6 @@ params {
     config_profile_name        = 'SOFT matrix track test profile'
     config_profile_description = 'Minimal settings for test of the SOFT matrix track'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/testdata/GSE50790.csv'
     contrasts = 'https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/testdata/GSE50790_contrasts.csv'

diff --git a/modules.json b/modules.json
@@ -7,27 +7,27 @@
                 "nf-core": {
                     "affy/justrma": {
                         "branch": "master",
-                        "git_sha": "02a65e8871e06bac203dec16985fa3de648c99b6",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "atlasgeneannotationmanipulation/gtf2featureannotation": {
                         "branch": "master",
-                        "git_sha": "04bc484c987b523ea5420ed6bbc1fdc6d8aef751",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "custom/matrixfilter": {
                         "branch": "master",
-                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "custom/tabulartogseacls": {
                         "branch": "master",
-                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "custom/tabulartogseagct": {
                         "branch": "master",
-                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "deseq2/differential": {
@@ -37,67 +37,67 @@
                     },
                     "geoquery/getgeo": {
                         "branch": "master",
-                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "gprofiler2/gost": {
                         "branch": "master",
-                        "git_sha": "c75e76bff35e2ee5305ebe89b513637b38e79d1d",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "gsea/gsea": {
                         "branch": "master",
-                        "git_sha": "7aa7ced253469386f0645133ec3e838098dbe67c",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "limma/differential": {
                         "branch": "master",
-                        "git_sha": "2ccee1830c4b65b9158f5750408ddfb6c7b12e9a",
+                        "git_sha": "136f443c0a6d5c526410c7c9b73ce51ef457c341",
                         "installed_by": ["modules"]
                     },
                     "proteus/readproteingroups": {
                         "branch": "master",
-                        "git_sha": "a069b29783583c219c1f23ed3dcf64a5aee1340b",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "rmarkdownnotebook": {
                         "branch": "master",
-                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/app": {
                         "branch": "master",
-                        "git_sha": "91fc36585a50f9bae98cb5b3dff36ce64c83a6b4",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/staticdifferential": {
                         "branch": "master",
-                        "git_sha": "91fc36585a50f9bae98cb5b3dff36ce64c83a6b4",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/staticexploratory": {
                         "branch": "master",
-                        "git_sha": "91fc36585a50f9bae98cb5b3dff36ce64c83a6b4",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/validatefomcomponents": {
                         "branch": "master",
-                        "git_sha": "91fc36585a50f9bae98cb5b3dff36ce64c83a6b4",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "zip": {
                         "branch": "master",
-                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     }
                 }
@@ -106,17 +106,17 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
+                        "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
+                        "git_sha": "d588e574e40a8aeba3636e2b766358091bfa3aa0",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
+                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
                         "installed_by": ["subworkflows"]
                     }
                 }

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/affy/justrma/templates/affy_justrma.R b/modules/nf-core/affy/justrma/templates/affy_justrma.R