Updated subworkflows, modules and test snaps

nf-core · Nov 22, 2024 · 9d910ea · 9d910ea
1 parent bc40764
commit 9d910ea
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Showing 15 changed files with 130 additions and 128 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#100](https://github.com/nf-core/nanostring/pull/100) - Added nf-tests for local module `NACHO_QC`.
 - [#101](https://github.com/nf-core/nanostring/pull/101) - Added nf-tests for local module `COMPUTE_GENE_SCORES`.
 - [#102](https://github.com/nf-core/nanostring/pull/102) - Added nf-tests for local module `CREATE_GENE_HEATMAP`.
+- [#104](https://github.com/nf-core/nanostring/pull/104) - Update all nf-core modules and subworkflows.
 
 ### `Fixed`
 

diff --git a/conf/base.config b/conf/base.config
@@ -10,7 +10,6 @@
 
 process {
 
-    // TODO nf-core: Check the defaults for all processes
     cpus   = { 1      * task.attempt }
     memory = { 6.GB   * task.attempt }
     time   = { 4.h    * task.attempt }

diff --git a/modules.json b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "fb387b16025333f6d66b88d6c48c3719f47b1637",
+                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     }
                 }
@@ -16,7 +16,7 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
+                        "git_sha": "56372688d8979092cafbe0c5c3895b491166ca1c",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
@@ -26,7 +26,7 @@
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
+                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
                         "installed_by": ["subworkflows"]
                     }
                 }

diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config
diff --git a/nextflow.config b/nextflow.config
@@ -177,7 +177,6 @@ profiles {
 includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
 
 // Load nf-core/nanostring custom profiles from different institutions.
-// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
 // includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/nanostring.config" : "/dev/null"
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile

diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap
@@ -70,26 +70,20 @@
                 "gene_heatmaps/gene_heatmap_mqc.png",
                 "multiqc",
                 "multiqc/multiqc_data",
-                "multiqc/multiqc_data/multiqc_Norm_GEX_ENDO-section-plot.txt",
-                "multiqc/multiqc_data/multiqc_Norm_GEX_HK-section-plot.txt",
+                "multiqc/multiqc_data/multiqc.log",
+                "multiqc/multiqc_data/multiqc_Norm_GEX_ENDO.txt",
+                "multiqc/multiqc_data/multiqc_Norm_GEX_ENDO_1.txt",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
-                "multiqc/multiqc_data/multiqc_normalized_qc-section-plot.txt",
                 "multiqc/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/multiqc_data/multiqc_sources.txt",
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_plots/pdf",
-                "multiqc/multiqc_plots/pdf/Norm_GEX_ENDO-section-plot.pdf",
-                "multiqc/multiqc_plots/pdf/Norm_GEX_HK-section-plot.pdf",
-                "multiqc/multiqc_plots/pdf/normalized_qc-section-plot.pdf",
+                "multiqc/multiqc_plots/pdf/Norm_GEX_ENDO.pdf",
                 "multiqc/multiqc_plots/png",
-                "multiqc/multiqc_plots/png/Norm_GEX_ENDO-section-plot.png",
-                "multiqc/multiqc_plots/png/Norm_GEX_HK-section-plot.png",
-                "multiqc/multiqc_plots/png/normalized_qc-section-plot.png",
+                "multiqc/multiqc_plots/png/Norm_GEX_ENDO.png",
                 "multiqc/multiqc_plots/svg",
-                "multiqc/multiqc_plots/svg/Norm_GEX_ENDO-section-plot.svg",
-                "multiqc/multiqc_plots/svg/Norm_GEX_HK-section-plot.svg",
-                "multiqc/multiqc_plots/svg/normalized_qc-section-plot.svg",
+                "multiqc/multiqc_plots/svg/Norm_GEX_ENDO.svg",
                 "multiqc/multiqc_report.html",
                 "normalized_counts",
                 "pipeline_info",
@@ -106,15 +100,16 @@
                 "PCAi_mqc.png:md5,2338d5fe0e447fc74d4969725546c136",
                 "POSF_vs_NEGF_mqc.png:md5,0e1b5105e68a6e0c51471afce218abdb",
                 "plot_normf_mqc.png:md5,6ffd3c11f8f5ddfbd3715e1780b10b01",
+                "multiqc_Norm_GEX_ENDO.txt:md5,215491482edeafbe25c4ef5f3e3b0a70",
+                "multiqc_Norm_GEX_ENDO_1.txt:md5,37174443be89fecb3d2de05bfa06169a",
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-                "multiqc_normalized_qc-section-plot.txt:md5,215491482edeafbe25c4ef5f3e3b0a70",
                 "multiqc_sources.txt:md5,d2a044df39ce3c6abe5cdc2d67473490"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-19T21:23:55.334879021"
+        "timestamp": "2024-11-22T14:03:55.044702369"
     }
-}
+}