Add opt-in feature gpu (#3562)

* optin

* [automated] Update CHANGELOG.md

* restructured the features, add GPU and downstream sample sheet, turned off features as defaut

* all features are on except for gpu

* update snapshot

* test snaps

* remove downstream_samplesheet feature

* remove unwanted log.txt

* use feature sections to classify the switches

* update yq command to read new template_features.yml structure

* update tests accessing template_features.yml

* fix yq command

* fix getting skip paths

* fix lint_config

* fix linting config again

* fix nf-test linting when nf-test is skipped

* fix nf-test snapshots for non nf-core pipelines

* more test snapshots fixes

* last pipeline test snapshot fixes

* update pytest snapshots

* update pytest snapshots

* fix test_customisation_help snapshot

* fix toggle_all binding

* Update nf_core/pipelines/create/create.py

Co-authored-by: Matthias Hörtenhuber <[email protected]>

* formatting

* debug

* debug

* Update nf_core/pipelines/create/custompipeline.py

Co-authored-by: Matthias Hörtenhuber <[email protected]>

* pre-commit

* [automated] Update Textual snapshots

* snapshotupdate

* [automated] Update Textual snapshots

* snapshot update from gitpod

---------

Co-authored-by: nf-core-bot <[email protected]>
Co-authored-by: Matthias Hörtenhuber <[email protected]>
Co-authored-by: Júlia Mir Pedrol <[email protected]>

Author: 4 people

.github/snapshots/adaptivecard.nf.test.snap

@@ -2,7 +2,14 @@
     "-profile test": {
         "content": [
             4,
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+                }
+            },
             [
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                 "fastqc/SAMPLE1_PE_1_fastqc.html",

.github/snapshots/changelog.nf.test.snap

@@ -2,7 +2,14 @@
     "-profile test": {
         "content": [
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+                }
+            },
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.github/snapshots/ci.nf.test.snap

@@ -2,7 +2,14 @@
     "-profile test": {
         "content": [
             4,
-            null,
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+                }
+            },
             [
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.github/snapshots/citations.nf.test.snap

@@ -2,7 +2,14 @@
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.github/snapshots/code_linters.nf.test.snap

@@ -2,7 +2,14 @@
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             [
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.github/snapshots/codespaces.nf.test.snap

@@ -2,7 +2,14 @@
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-            null,
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+                }
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             [
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.github/snapshots/documentation.nf.test.snap

@@ -2,7 +2,14 @@
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             4,
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.github/snapshots/email.nf.test.snap

@@ -2,7 +2,14 @@
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                 "fastqc/SAMPLE1_PE_1_fastqc.html",

.github/snapshots/fastqc.nf.test.snap

@@ -2,7 +2,11 @@
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.github/snapshots/github_badges.nf.test.snap

@@ -2,7 +2,14 @@
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+                }
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             [
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                 "fastqc/SAMPLE1_PE_1_fastqc.html",