Merge branch 'dev' into fresh-nf-test

nf-core · Oct 15, 2024 · 245d355 · 245d355
2 parents f470227 + 96f6366
commit 245d355
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Showing 6 changed files with 16 additions and 10 deletions.
diff --git a/.gitignore b/.gitignore
@@ -6,6 +6,7 @@ results/
 testing/
 testing*
 *.pyc
+null/
 *.code-workspace
 .nf-test*
 .nf-test/

diff --git a/.nf-core.yml b/.nf-core.yml
@@ -12,7 +12,7 @@ lint:
     - docs/images/nf-core-sarek_logo_light.png
   modules_config: false
   template_strings: false
-nf_core_version: 3.0.1
+nf_core_version: 3.0.2
 org_path: null
 repository_type: pipeline
 template:

diff --git a/modules.json b/modules.json
@@ -346,7 +346,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c",
+                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     },
                     "ngscheckmate/ncm": {
@@ -515,7 +515,7 @@
                     },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
+                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {

diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf
@@ -52,7 +52,6 @@ workflow PIPELINE_INITIALISATION {
         workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
     )
 
-
     //
     // Validate parameters and generate parameter summary to stdout
     //
@@ -62,7 +61,6 @@ workflow PIPELINE_INITIALISATION {
         null
     )
 
-
     //
     // Check config provided to the pipeline
     //
@@ -177,7 +175,6 @@ workflow PIPELINE_COMPLETION {
     email           //  string: email address
     email_on_fail   //  string: email address sent on pipeline failure
     plaintext_email // boolean: Send plain-text email instead of HTML
-
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
     hook_url        //  string: hook URL for notifications

diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf