diff --git a/.github/workflows/update-textual-snapshots.yml b/.github/workflows/update-textual-snapshots.yml
index fb936762f..2adb1b8d8 100644
--- a/.github/workflows/update-textual-snapshots.yml
+++ b/.github/workflows/update-textual-snapshots.yml
@@ -46,7 +46,7 @@ jobs:
- name: Run pytest to update snapshots
id: pytest
run: |
- python3 -m pytest tests/test_create_app.py --snapshot-update --color=yes --durations=0
+ python3 -m pytest tests/pipelines/test_create_app.py --snapshot-update --color=yes --durations=0
continue-on-error: true
# indication that the run has finished
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index f9773296c..ce3635433 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -153,7 +153,7 @@ Optionally followed by the description that you want to add to the changelog.
- Update Textual snapshots:
-If the Textual snapshots (run by `tests/test_crate_app.py`) fail, an HTML report is generated and uploaded as an artifact.
+If the Textual snapshots (run by `tests/pipelines/test_crate_app.py`) fail, an HTML report is generated and uploaded as an artifact.
If you are sure that these changes are correct, you can automatically update the snapshots form the PR by posting a comment with the magic words:
```
diff --git a/nf_core/utils.py b/nf_core/utils.py
index 068da22de..87dd307e7 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -323,7 +323,7 @@ def fetch_wf_config(wf_path: Path, cache_config: bool = True) -> dict:
# If we can, save a cached copy
# HINT: during testing phase (in test_download, for example) we don't want
- # to save configuration copy in $HOME, otherwise the tests/test_download.py::DownloadTest::test_wf_use_local_configs
+ # to save configuration copy in $HOME, otherwise the tests/pipelines/test_download.py::DownloadTest::test_wf_use_local_configs
# will fail after the first attempt. It's better to not save temporary data
# in others folders than tmp when doing tests in general
if cache_path and cache_config:
diff --git a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg
index 0e1682290..f327dac79 100644
--- a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg
+++ b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg
@@ -19,253 +19,253 @@
font-weight: 700;
}
- .terminal-1305977867-matrix {
+ .terminal-1837969819-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-1305977867-title {
+ .terminal-1837969819-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-1305977867-r1 { fill: #c5c8c6 }
-.terminal-1305977867-r2 { fill: #e3e3e3 }
-.terminal-1305977867-r3 { fill: #989898 }
-.terminal-1305977867-r4 { fill: #e1e1e1 }
-.terminal-1305977867-r5 { fill: #4ebf71;font-weight: bold }
-.terminal-1305977867-r6 { fill: #a5a5a5;font-style: italic; }
-.terminal-1305977867-r7 { fill: #1e1e1e }
-.terminal-1305977867-r8 { fill: #008139 }
-.terminal-1305977867-r9 { fill: #121212 }
-.terminal-1305977867-r10 { fill: #e2e2e2 }
-.terminal-1305977867-r11 { fill: #787878 }
-.terminal-1305977867-r12 { fill: #454a50 }
-.terminal-1305977867-r13 { fill: #7ae998 }
-.terminal-1305977867-r14 { fill: #e2e3e3;font-weight: bold }
-.terminal-1305977867-r15 { fill: #0a180e;font-weight: bold }
-.terminal-1305977867-r16 { fill: #000000 }
-.terminal-1305977867-r17 { fill: #fea62b;font-weight: bold }
-.terminal-1305977867-r18 { fill: #a7a9ab }
-.terminal-1305977867-r19 { fill: #e2e3e3 }
+ .terminal-1837969819-r1 { fill: #c5c8c6 }
+.terminal-1837969819-r2 { fill: #e3e3e3 }
+.terminal-1837969819-r3 { fill: #989898 }
+.terminal-1837969819-r4 { fill: #e1e1e1 }
+.terminal-1837969819-r5 { fill: #4ebf71;font-weight: bold }
+.terminal-1837969819-r6 { fill: #a5a5a5;font-style: italic; }
+.terminal-1837969819-r7 { fill: #1e1e1e }
+.terminal-1837969819-r8 { fill: #008139 }
+.terminal-1837969819-r9 { fill: #121212 }
+.terminal-1837969819-r10 { fill: #e2e2e2 }
+.terminal-1837969819-r11 { fill: #787878 }
+.terminal-1837969819-r12 { fill: #454a50 }
+.terminal-1837969819-r13 { fill: #7ae998 }
+.terminal-1837969819-r14 { fill: #e2e3e3;font-weight: bold }
+.terminal-1837969819-r15 { fill: #0a180e;font-weight: bold }
+.terminal-1837969819-r16 { fill: #000000 }
+.terminal-1837969819-r17 { fill: #fea62b;font-weight: bold }
+.terminal-1837969819-r18 { fill: #a7a9ab }
+.terminal-1837969819-r19 { fill: #e2e3e3 }
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- nf-core pipelines create
+ nf-core pipelines create
-
-
-
- ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
-
-
-Basic details
-
-
-
-
-GitHub organisationWorkflow name
-
-▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎
-▊nf-core▎▊Pipeline Name▎
-▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
-
-
-
-A short description of your pipeline.
-
-▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎
-▊Description▎
-▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
-
-
-
-Name of the main author / authors
-
-▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎
-▊Author(s)▎
-▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
-
-▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
- Back Next
-▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
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-
-
-
- d Toggle dark mode q Quit
+
+
+
+ ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
+
+
+Basic details
+
+
+
+
+GitHub organisationWorkflow name
+
+▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎
+▊nf-core▎▊Pipeline Name▎
+▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
+
+
+
+A short description of your pipeline.
+
+▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎
+▊Description▎
+▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
+
+
+
+Name of the main author / authors
+
+▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎
+▊Author(s)▎
+▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
+
+▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ Back Next
+▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
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+ d Toggle dark mode q Quit a Toggle all
diff --git a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg
index 02f4fc213..6a4e42413 100644
--- a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg
+++ b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg
@@ -19,256 +19,256 @@
font-weight: 700;
}
- .terminal-667641811-matrix {
+ .terminal-2735207764-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-667641811-title {
+ .terminal-2735207764-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-667641811-r1 { fill: #c5c8c6 }
-.terminal-667641811-r2 { fill: #e3e3e3 }
-.terminal-667641811-r3 { fill: #989898 }
-.terminal-667641811-r4 { fill: #e1e1e1 }
-.terminal-667641811-r5 { fill: #4ebf71;font-weight: bold }
-.terminal-667641811-r6 { fill: #a5a5a5;font-style: italic; }
-.terminal-667641811-r7 { fill: #1e1e1e }
-.terminal-667641811-r8 { fill: #0f4e2a }
-.terminal-667641811-r9 { fill: #0178d4 }
-.terminal-667641811-r10 { fill: #a7a7a7 }
-.terminal-667641811-r11 { fill: #787878 }
-.terminal-667641811-r12 { fill: #e2e2e2 }
-.terminal-667641811-r13 { fill: #121212 }
-.terminal-667641811-r14 { fill: #454a50 }
-.terminal-667641811-r15 { fill: #7ae998 }
-.terminal-667641811-r16 { fill: #e2e3e3;font-weight: bold }
-.terminal-667641811-r17 { fill: #0a180e;font-weight: bold }
-.terminal-667641811-r18 { fill: #000000 }
-.terminal-667641811-r19 { fill: #008139 }
-.terminal-667641811-r20 { fill: #fea62b;font-weight: bold }
-.terminal-667641811-r21 { fill: #a7a9ab }
-.terminal-667641811-r22 { fill: #e2e3e3 }
+ .terminal-2735207764-r1 { fill: #c5c8c6 }
+.terminal-2735207764-r2 { fill: #e3e3e3 }
+.terminal-2735207764-r3 { fill: #989898 }
+.terminal-2735207764-r4 { fill: #e1e1e1 }
+.terminal-2735207764-r5 { fill: #4ebf71;font-weight: bold }
+.terminal-2735207764-r6 { fill: #a5a5a5;font-style: italic; }
+.terminal-2735207764-r7 { fill: #1e1e1e }
+.terminal-2735207764-r8 { fill: #0f4e2a }
+.terminal-2735207764-r9 { fill: #0178d4 }
+.terminal-2735207764-r10 { fill: #a7a7a7 }
+.terminal-2735207764-r11 { fill: #787878 }
+.terminal-2735207764-r12 { fill: #e2e2e2 }
+.terminal-2735207764-r13 { fill: #121212 }
+.terminal-2735207764-r14 { fill: #454a50 }
+.terminal-2735207764-r15 { fill: #7ae998 }
+.terminal-2735207764-r16 { fill: #e2e3e3;font-weight: bold }
+.terminal-2735207764-r17 { fill: #0a180e;font-weight: bold }
+.terminal-2735207764-r18 { fill: #000000 }
+.terminal-2735207764-r19 { fill: #008139 }
+.terminal-2735207764-r20 { fill: #fea62b;font-weight: bold }
+.terminal-2735207764-r21 { fill: #a7a9ab }
+.terminal-2735207764-r22 { fill: #e2e3e3 }
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- nf-core pipelines create
+ nf-core pipelines create
-
-
-
- ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
-
-
-Basic details
-
-
-
-
-GitHub organisationWorkflow name
-
-▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎
-▊nf-core ▎▊Pipeline Name▎
-▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
-
-
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-A short description of your pipeline.
-
-▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎
-▊Description▎
-▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
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-Name of the main author / authors
-
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-▊Author(s)▎
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- Back Next
-▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
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- d Toggle dark mode q Quit
+
+
+
+ ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
+
+
+Basic details
+
+
+
+
+GitHub organisationWorkflow name
+
+▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎
+▊nf-core ▎▊Pipeline Name▎
+▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
+
+
+
+A short description of your pipeline.
+
+▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎
+▊Description▎
+▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
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+Name of the main author / authors
+
+▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎
+▊Author(s)▎
+▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
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+ Back Next
+▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
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diff --git a/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg b/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg
index 73ba989e0..3eaceeb47 100644
--- a/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg
+++ b/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg
@@ -19,251 +19,251 @@
font-weight: 700;
}
- .terminal-2396773597-matrix {
+ .terminal-2526112365-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-2396773597-title {
+ .terminal-2526112365-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-2396773597-r1 { fill: #c5c8c6 }
-.terminal-2396773597-r2 { fill: #e3e3e3 }
-.terminal-2396773597-r3 { fill: #989898 }
-.terminal-2396773597-r4 { fill: #e1e1e1 }
-.terminal-2396773597-r5 { fill: #4ebf71;font-weight: bold }
-.terminal-2396773597-r6 { fill: #4ebf71;text-decoration: underline; }
-.terminal-2396773597-r7 { fill: #4ebf71;font-style: italic;;text-decoration: underline; }
-.terminal-2396773597-r8 { fill: #e1e1e1;font-style: italic; }
-.terminal-2396773597-r9 { fill: #7ae998 }
-.terminal-2396773597-r10 { fill: #008139 }
-.terminal-2396773597-r11 { fill: #507bb3 }
-.terminal-2396773597-r12 { fill: #dde6ed;font-weight: bold }
-.terminal-2396773597-r13 { fill: #001541 }
-.terminal-2396773597-r14 { fill: #e1e1e1;text-decoration: underline; }
-.terminal-2396773597-r15 { fill: #fea62b;font-weight: bold }
-.terminal-2396773597-r16 { fill: #a7a9ab }
-.terminal-2396773597-r17 { fill: #e2e3e3 }
+ .terminal-2526112365-r1 { fill: #c5c8c6 }
+.terminal-2526112365-r2 { fill: #e3e3e3 }
+.terminal-2526112365-r3 { fill: #989898 }
+.terminal-2526112365-r4 { fill: #e1e1e1 }
+.terminal-2526112365-r5 { fill: #4ebf71;font-weight: bold }
+.terminal-2526112365-r6 { fill: #4ebf71;text-decoration: underline; }
+.terminal-2526112365-r7 { fill: #4ebf71;font-style: italic;;text-decoration: underline; }
+.terminal-2526112365-r8 { fill: #e1e1e1;font-style: italic; }
+.terminal-2526112365-r9 { fill: #7ae998 }
+.terminal-2526112365-r10 { fill: #008139 }
+.terminal-2526112365-r11 { fill: #507bb3 }
+.terminal-2526112365-r12 { fill: #dde6ed;font-weight: bold }
+.terminal-2526112365-r13 { fill: #001541 }
+.terminal-2526112365-r14 { fill: #e1e1e1;text-decoration: underline; }
+.terminal-2526112365-r15 { fill: #fea62b;font-weight: bold }
+.terminal-2526112365-r16 { fill: #a7a9ab }
+.terminal-2526112365-r17 { fill: #e2e3e3 }
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- nf-core pipelines create
+ nf-core pipelines create
-
-
-
- ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
-
-
-Choose pipeline type
-
-
-
-
-Choose "nf-core" if:Choose "Custom" if:
-
-● You want your pipeline to be part of the ● Your pipeline will never be part of
-nf-core communitynf-core
-● You think that there's an outside chance ● You want full control over all features
-that it ever could be part of nf-corethat are included from the template
-(including those that are mandatory for
-nf-core).
-▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
- nf-core
-▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
- Custom
-▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-
-
-
-
-What's the difference?
-
- Choosing "nf-core" effectively pre-selects the following template features:
-
-● GitHub Actions continuous-integration configuration files:
-▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS)
-▪ Code formatting checks with Prettier
-▪ Auto-fix linting functionality using @nf-core-bot
-▪ Marking old issues as stale
-● Inclusion of shared nf-core configuration profiles
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- d Toggle dark mode q Quit
+
+
+
+ ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
+
+
+Choose pipeline type
+
+
+
+
+Choose "nf-core" if:Choose "Custom" if:
+
+● You want your pipeline to be part of the ● Your pipeline will never be part of
+nf-core communitynf-core
+● You think that there's an outside chance ● You want full control over all features
+that it ever could be part of nf-corethat are included from the template
+(including those that are mandatory for
+nf-core).
+▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ nf-core
+▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ Custom
+▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+
+
+
+
+What's the difference?
+
+ Choosing "nf-core" effectively pre-selects the following template features:
+
+● GitHub Actions continuous-integration configuration files:
+▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS)
+▪ Code formatting checks with Prettier
+▪ Auto-fix linting functionality using @nf-core-bot
+▪ Marking old issues as stale
+● Inclusion of shared nf-core configuration profiles
+
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+ d Toggle dark mode q Quit a Toggle all
diff --git a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg
index d469a4761..f86647d78 100644
--- a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg
+++ b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg
@@ -19,257 +19,257 @@
font-weight: 700;
}
- .terminal-2979952766-matrix {
+ .terminal-1327302158-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-2979952766-title {
+ .terminal-1327302158-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-2979952766-r1 { fill: #c5c8c6 }
-.terminal-2979952766-r2 { fill: #e3e3e3 }
-.terminal-2979952766-r3 { fill: #989898 }
-.terminal-2979952766-r4 { fill: #e1e1e1 }
-.terminal-2979952766-r5 { fill: #4ebf71;font-weight: bold }
-.terminal-2979952766-r6 { fill: #1e1e1e }
-.terminal-2979952766-r7 { fill: #507bb3 }
-.terminal-2979952766-r8 { fill: #e2e2e2 }
-.terminal-2979952766-r9 { fill: #808080 }
-.terminal-2979952766-r10 { fill: #dde6ed;font-weight: bold }
-.terminal-2979952766-r11 { fill: #001541 }
-.terminal-2979952766-r12 { fill: #14191f }
-.terminal-2979952766-r13 { fill: #0178d4 }
-.terminal-2979952766-r14 { fill: #454a50 }
-.terminal-2979952766-r15 { fill: #e2e3e3;font-weight: bold }
-.terminal-2979952766-r16 { fill: #000000 }
-.terminal-2979952766-r17 { fill: #e4e4e4 }
-.terminal-2979952766-r18 { fill: #7ae998 }
-.terminal-2979952766-r19 { fill: #0a180e;font-weight: bold }
-.terminal-2979952766-r20 { fill: #008139 }
-.terminal-2979952766-r21 { fill: #fea62b;font-weight: bold }
-.terminal-2979952766-r22 { fill: #a7a9ab }
-.terminal-2979952766-r23 { fill: #e2e3e3 }
+ .terminal-1327302158-r1 { fill: #c5c8c6 }
+.terminal-1327302158-r2 { fill: #e3e3e3 }
+.terminal-1327302158-r3 { fill: #989898 }
+.terminal-1327302158-r4 { fill: #e1e1e1 }
+.terminal-1327302158-r5 { fill: #4ebf71;font-weight: bold }
+.terminal-1327302158-r6 { fill: #1e1e1e }
+.terminal-1327302158-r7 { fill: #507bb3 }
+.terminal-1327302158-r8 { fill: #e2e2e2 }
+.terminal-1327302158-r9 { fill: #808080 }
+.terminal-1327302158-r10 { fill: #dde6ed;font-weight: bold }
+.terminal-1327302158-r11 { fill: #001541 }
+.terminal-1327302158-r12 { fill: #14191f }
+.terminal-1327302158-r13 { fill: #0178d4 }
+.terminal-1327302158-r14 { fill: #454a50 }
+.terminal-1327302158-r15 { fill: #e2e3e3;font-weight: bold }
+.terminal-1327302158-r16 { fill: #000000 }
+.terminal-1327302158-r17 { fill: #e4e4e4 }
+.terminal-1327302158-r18 { fill: #7ae998 }
+.terminal-1327302158-r19 { fill: #0a180e;font-weight: bold }
+.terminal-1327302158-r20 { fill: #008139 }
+.terminal-1327302158-r21 { fill: #fea62b;font-weight: bold }
+.terminal-1327302158-r22 { fill: #a7a9ab }
+.terminal-1327302158-r23 { fill: #e2e3e3 }
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- nf-core pipelines create
+ nf-core pipelines create
-
-
-
- ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
-
-
-Template features
-
-
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Use a GitHub Create a GitHub Show help
-▊▁▁▁▁▁▁▁▁▎ repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-pipeline.
-
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Add Github CI testsThe pipeline will Show help
-▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-actions for Continuous
-Integration (CI)
-testing▄▄
-
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Use reference genomesThe pipeline will be Hide help
-▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-copy of the most
-common reference
-genome files from
-iGenomes
-
-
-Nf-core pipelines are configured to use a copy of the most common reference
-genome files.
-
-By selecting this option, your pipeline will include a configuration file
-specifying the paths to these files.
-
-The required code to use these files will also be included in the template.
-When the pipeline user provides an appropriate genome key, the pipeline will
-automatically download the required reference files.
-▅▅
-For more information about reference genomes in nf-core pipelines, see the
-
-
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Add Github badgesThe README.md file of Show help
-▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-include GitHub badges
-
-▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
- Back Continue
-▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-
- d Toggle dark mode q Quit
+
+
+
+ ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
+
+
+Template features
+
+
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Use a GitHub Create a GitHub Show help
+▊▁▁▁▁▁▁▁▁▎ repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+pipeline.
+
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Add Github CI testsThe pipeline will Show help
+▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+actions for Continuous
+Integration (CI)
+testing▄▄
+
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Use reference genomesThe pipeline will be Hide help
+▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+copy of the most
+common reference
+genome files from
+iGenomes
+
+
+Nf-core pipelines are configured to use a copy of the most common reference
+genome files.
+
+By selecting this option, your pipeline will include a configuration file
+specifying the paths to these files.
+
+The required code to use these files will also be included in the template.
+When the pipeline user provides an appropriate genome key, the pipeline will
+automatically download the required reference files.
+▅▅
+For more information about reference genomes in nf-core pipelines, see the
+
+
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Add Github badgesThe README.md file of Show help
+▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+include GitHub badges
+
+▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ Back Continue
+▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+
+ d Toggle dark mode q Quit a Toggle all
diff --git a/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg b/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg
index b34483176..74c232f74 100644
--- a/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg
+++ b/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg
@@ -19,251 +19,251 @@
font-weight: 700;
}
- .terminal-610734766-matrix {
+ .terminal-3905134639-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-610734766-title {
+ .terminal-3905134639-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-610734766-r1 { fill: #c5c8c6 }
-.terminal-610734766-r2 { fill: #e3e3e3 }
-.terminal-610734766-r3 { fill: #989898 }
-.terminal-610734766-r4 { fill: #e1e1e1 }
-.terminal-610734766-r5 { fill: #4ebf71;font-weight: bold }
-.terminal-610734766-r6 { fill: #a5a5a5;font-style: italic; }
-.terminal-610734766-r7 { fill: #1e1e1e }
-.terminal-610734766-r8 { fill: #008139 }
-.terminal-610734766-r9 { fill: #e2e2e2 }
-.terminal-610734766-r10 { fill: #454a50 }
-.terminal-610734766-r11 { fill: #7ae998 }
-.terminal-610734766-r12 { fill: #e2e3e3;font-weight: bold }
-.terminal-610734766-r13 { fill: #0a180e;font-weight: bold }
-.terminal-610734766-r14 { fill: #000000 }
-.terminal-610734766-r15 { fill: #fea62b;font-weight: bold }
-.terminal-610734766-r16 { fill: #a7a9ab }
-.terminal-610734766-r17 { fill: #e2e3e3 }
+ .terminal-3905134639-r1 { fill: #c5c8c6 }
+.terminal-3905134639-r2 { fill: #e3e3e3 }
+.terminal-3905134639-r3 { fill: #989898 }
+.terminal-3905134639-r4 { fill: #e1e1e1 }
+.terminal-3905134639-r5 { fill: #4ebf71;font-weight: bold }
+.terminal-3905134639-r6 { fill: #a5a5a5;font-style: italic; }
+.terminal-3905134639-r7 { fill: #1e1e1e }
+.terminal-3905134639-r8 { fill: #008139 }
+.terminal-3905134639-r9 { fill: #e2e2e2 }
+.terminal-3905134639-r10 { fill: #454a50 }
+.terminal-3905134639-r11 { fill: #7ae998 }
+.terminal-3905134639-r12 { fill: #e2e3e3;font-weight: bold }
+.terminal-3905134639-r13 { fill: #0a180e;font-weight: bold }
+.terminal-3905134639-r14 { fill: #000000 }
+.terminal-3905134639-r15 { fill: #fea62b;font-weight: bold }
+.terminal-3905134639-r16 { fill: #a7a9ab }
+.terminal-3905134639-r17 { fill: #e2e3e3 }
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+
- nf-core pipelines create
+ nf-core pipelines create
-
-
-
- ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
-
-
-Final details
-
-
-
-
-First version of the pipelinePath to the output directory where the
-pipeline will be created
-▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎
-▊1.0.0dev▎▊. ▎
-▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
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-▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
- Back Finish
-▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
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-
- d Toggle dark mode q Quit
+
+
+
+ ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
+
+
+Final details
+
+
+
+
+First version of the pipelinePath to the output directory where the
+pipeline will be created
+▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎
+▊1.0.0dev▎▊. ▎
+▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
+
+▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ Back Finish
+▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
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+
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+
+ d Toggle dark mode q Quit a Toggle all
diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg
index 9276d5348..77a293fb7 100644
--- a/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg
+++ b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg
@@ -19,258 +19,258 @@
font-weight: 700;
}
- .terminal-1772902547-matrix {
+ .terminal-661775892-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-1772902547-title {
+ .terminal-661775892-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-1772902547-r1 { fill: #c5c8c6 }
-.terminal-1772902547-r2 { fill: #e3e3e3 }
-.terminal-1772902547-r3 { fill: #989898 }
-.terminal-1772902547-r4 { fill: #e1e1e1 }
-.terminal-1772902547-r5 { fill: #4ebf71;font-weight: bold }
-.terminal-1772902547-r6 { fill: #a5a5a5;font-style: italic; }
-.terminal-1772902547-r7 { fill: #454a50 }
-.terminal-1772902547-r8 { fill: #e2e3e3;font-weight: bold }
-.terminal-1772902547-r9 { fill: #1e1e1e }
-.terminal-1772902547-r10 { fill: #008139 }
-.terminal-1772902547-r11 { fill: #000000 }
-.terminal-1772902547-r12 { fill: #e2e2e2 }
-.terminal-1772902547-r13 { fill: #18954b }
-.terminal-1772902547-r14 { fill: #e2e2e2;font-weight: bold }
-.terminal-1772902547-r15 { fill: #969696;font-weight: bold }
-.terminal-1772902547-r16 { fill: #808080 }
-.terminal-1772902547-r17 { fill: #7ae998 }
-.terminal-1772902547-r18 { fill: #507bb3 }
-.terminal-1772902547-r19 { fill: #0a180e;font-weight: bold }
-.terminal-1772902547-r20 { fill: #dde6ed;font-weight: bold }
-.terminal-1772902547-r21 { fill: #001541 }
-.terminal-1772902547-r22 { fill: #fea62b;font-weight: bold }
-.terminal-1772902547-r23 { fill: #a7a9ab }
-.terminal-1772902547-r24 { fill: #e2e3e3 }
+ .terminal-661775892-r1 { fill: #c5c8c6 }
+.terminal-661775892-r2 { fill: #e3e3e3 }
+.terminal-661775892-r3 { fill: #989898 }
+.terminal-661775892-r4 { fill: #e1e1e1 }
+.terminal-661775892-r5 { fill: #4ebf71;font-weight: bold }
+.terminal-661775892-r6 { fill: #a5a5a5;font-style: italic; }
+.terminal-661775892-r7 { fill: #454a50 }
+.terminal-661775892-r8 { fill: #e2e3e3;font-weight: bold }
+.terminal-661775892-r9 { fill: #1e1e1e }
+.terminal-661775892-r10 { fill: #008139 }
+.terminal-661775892-r11 { fill: #000000 }
+.terminal-661775892-r12 { fill: #e2e2e2 }
+.terminal-661775892-r13 { fill: #18954b }
+.terminal-661775892-r14 { fill: #e2e2e2;font-weight: bold }
+.terminal-661775892-r15 { fill: #969696;font-weight: bold }
+.terminal-661775892-r16 { fill: #808080 }
+.terminal-661775892-r17 { fill: #7ae998 }
+.terminal-661775892-r18 { fill: #507bb3 }
+.terminal-661775892-r19 { fill: #0a180e;font-weight: bold }
+.terminal-661775892-r20 { fill: #dde6ed;font-weight: bold }
+.terminal-661775892-r21 { fill: #001541 }
+.terminal-661775892-r22 { fill: #fea62b;font-weight: bold }
+.terminal-661775892-r23 { fill: #a7a9ab }
+.terminal-661775892-r24 { fill: #e2e3e3 }
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+
- nf-core pipelines create
+ nf-core pipelines create
-
-
-
- ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
-
-
-Create GitHub repository
-
- Now that we have created a new pipeline locally, we can create a new GitHub repository and push
- the code to it.
-
-
-
-
-Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-for login. Show
-▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-▊GitHub username▎▊•••••••••••• ▎
-▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
-
-
-
-The name of the organisation where the The name of the new GitHub repository
-GitHub repo will be cretaed
-▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎
-▊nf-core ▎▊mypipeline ▎
-▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
-
-
-▌⚠️ You can't create a repository directly in the nf-core organisation.
-▌Please create the pipeline repo to an organisation where you have access or use your user
-▌account. A core-team member will be able to transfer the repo to nf-core once the development
-▌has started.
-
-▌💡 Your GitHub user account will be used by default if nf-core is given as the org name.
-
-
-▊▔▔▔▔▔▔▔▔▎Private
-▊▎Select to make the new GitHub repo private.
-▊▁▁▁▁▁▁▁▁▎
-▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
- Back Create GitHub repo Finish without creating a repo
-▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-
-
-
-
-
-
-
-
-
- d Toggle dark mode q Quit
+
+
+
+ ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
+
+
+Create GitHub repository
+
+ Now that we have created a new pipeline locally, we can create a new GitHub repository and push
+ the code to it.
+
+
+
+
+Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+for login. Show
+▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+▊GitHub username▎▊•••••••••••• ▎
+▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
+
+
+
+The name of the organisation where the The name of the new GitHub repository
+GitHub repo will be cretaed
+▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎
+▊nf-core ▎▊mypipeline ▎
+▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
+
+
+▌⚠️ You can't create a repository directly in the nf-core organisation.
+▌Please create the pipeline repo to an organisation where you have access or use your user
+▌account. A core-team member will be able to transfer the repo to nf-core once the development
+▌has started.
+
+▌💡 Your GitHub user account will be used by default if nf-core is given as the org name.
+
+
+▊▔▔▔▔▔▔▔▔▎Private
+▊▎Select to make the new GitHub repo private.
+▊▁▁▁▁▁▁▁▁▎
+▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ Back Create GitHub repo Finish without creating a repo
+▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+
+
+
+
+
+
+
+
+
+ d Toggle dark mode q Quit a Toggle all
diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg
index f840f8849..1be8c63f1 100644
--- a/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg
+++ b/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg
@@ -19,254 +19,254 @@
font-weight: 700;
}
- .terminal-1075265190-matrix {
+ .terminal-995675175-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-1075265190-title {
+ .terminal-995675175-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-1075265190-r1 { fill: #c5c8c6 }
-.terminal-1075265190-r2 { fill: #e3e3e3 }
-.terminal-1075265190-r3 { fill: #989898 }
-.terminal-1075265190-r4 { fill: #e1e1e1 }
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-.terminal-1075265190-r15 { fill: #969696;font-weight: bold }
-.terminal-1075265190-r16 { fill: #7ae998 }
-.terminal-1075265190-r17 { fill: #008139 }
-.terminal-1075265190-r18 { fill: #fea62b;font-weight: bold }
-.terminal-1075265190-r19 { fill: #a7a9ab }
-.terminal-1075265190-r20 { fill: #e2e3e3 }
+ .terminal-995675175-r1 { fill: #c5c8c6 }
+.terminal-995675175-r2 { fill: #e3e3e3 }
+.terminal-995675175-r3 { fill: #989898 }
+.terminal-995675175-r4 { fill: #e1e1e1 }
+.terminal-995675175-r5 { fill: #4ebf71;font-weight: bold }
+.terminal-995675175-r6 { fill: #98e024 }
+.terminal-995675175-r7 { fill: #626262 }
+.terminal-995675175-r8 { fill: #9d65ff }
+.terminal-995675175-r9 { fill: #fd971f }
+.terminal-995675175-r10 { fill: #d2d2d2 }
+.terminal-995675175-r11 { fill: #82aaff }
+.terminal-995675175-r12 { fill: #eeffff }
+.terminal-995675175-r13 { fill: #18954b }
+.terminal-995675175-r14 { fill: #e2e2e2 }
+.terminal-995675175-r15 { fill: #969696;font-weight: bold }
+.terminal-995675175-r16 { fill: #7ae998 }
+.terminal-995675175-r17 { fill: #008139 }
+.terminal-995675175-r18 { fill: #fea62b;font-weight: bold }
+.terminal-995675175-r19 { fill: #a7a9ab }
+.terminal-995675175-r20 { fill: #e2e3e3 }
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+
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+
- nf-core pipelines create
+ nf-core pipelines create
-
-
-
- ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
-
-
-HowTo create a GitHub repository
-
-
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
- If you would like to create the GitHub repository later, you can do it manually by following
- these steps:
-
- 1. Create a new GitHub repository
- 2. Add the remote to your local repository:
-
-
-cd <pipeline_directory>
-git remote add origin git@github.com:<username>/<repo_name>.git
-
-
- 3. Push the code to the remote:
-
-
-git push --all origin
-
-
-▌💡 Note the --all flag: this is needed to push all branches to the remote.
-
-
-
-▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
- Close
-▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-
-
-
-
-
-
-
-
-
-
-
-
- d Toggle dark mode q Quit
+
+
+
+ ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
+
+
+HowTo create a GitHub repository
+
+
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ If you would like to create the GitHub repository later, you can do it manually by following
+ these steps:
+
+ 1. Create a new GitHub repository
+ 2. Add the remote to your local repository:
+
+
+cd <pipeline_directory>
+git remote add origin git@github.com:<username>/<repo_name>.git
+
+
+ 3. Push the code to the remote:
+
+
+git push --all origin
+
+
+▌💡 Note the --all flag: this is needed to push all branches to the remote.
+
+
+
+▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ Close
+▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+
+
+
+
+
+
+
+
+
+
+
+
+ d Toggle dark mode q Quit a Toggle all
diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg
index f302feaae..8aad414e6 100644
--- a/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg
+++ b/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg
@@ -19,247 +19,247 @@
font-weight: 700;
}
- .terminal-3993718311-matrix {
+ .terminal-345103272-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-3993718311-title {
+ .terminal-345103272-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-3993718311-r1 { fill: #c5c8c6 }
-.terminal-3993718311-r2 { fill: #e3e3e3 }
-.terminal-3993718311-r3 { fill: #989898 }
-.terminal-3993718311-r4 { fill: #e1e1e1 }
-.terminal-3993718311-r5 { fill: #4ebf71;font-weight: bold }
-.terminal-3993718311-r6 { fill: #7ae998 }
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-.terminal-3993718311-r8 { fill: #dde6ed;font-weight: bold }
-.terminal-3993718311-r9 { fill: #008139 }
-.terminal-3993718311-r10 { fill: #001541 }
-.terminal-3993718311-r11 { fill: #fea62b;font-weight: bold }
-.terminal-3993718311-r12 { fill: #a7a9ab }
-.terminal-3993718311-r13 { fill: #e2e3e3 }
+ .terminal-345103272-r1 { fill: #c5c8c6 }
+.terminal-345103272-r2 { fill: #e3e3e3 }
+.terminal-345103272-r3 { fill: #989898 }
+.terminal-345103272-r4 { fill: #e1e1e1 }
+.terminal-345103272-r5 { fill: #4ebf71;font-weight: bold }
+.terminal-345103272-r6 { fill: #7ae998 }
+.terminal-345103272-r7 { fill: #507bb3 }
+.terminal-345103272-r8 { fill: #dde6ed;font-weight: bold }
+.terminal-345103272-r9 { fill: #008139 }
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+.terminal-345103272-r11 { fill: #fea62b;font-weight: bold }
+.terminal-345103272-r12 { fill: #a7a9ab }
+.terminal-345103272-r13 { fill: #e2e3e3 }
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+
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+
- nf-core pipelines create
+ nf-core pipelines create
-
-
-
- ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
-
-
-Create GitHub repository
-
-
- After creating the pipeline template locally, we can create a GitHub repository and push the
- code to it.
-
- Do you want to create a GitHub repository?
-
-
-▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
- Create GitHub repo Finish without creating a repo
-▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
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-
-
-
-
-
-
-
-
-
- d Toggle dark mode q Quit
+
+
+
+ ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
+
+
+Create GitHub repository
+
+
+ After creating the pipeline template locally, we can create a GitHub repository and push the
+ code to it.
+
+ Do you want to create a GitHub repository?
+
+
+▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ Create GitHub repo Finish without creating a repo
+▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
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+ d Toggle dark mode q Quit a Toggle all
diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg
index 399989e47..c8537c6d1 100644
--- a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg
+++ b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg
@@ -19,255 +19,255 @@
font-weight: 700;
}
- .terminal-3949666415-matrix {
+ .terminal-3873418736-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-3949666415-title {
+ .terminal-3873418736-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-3949666415-r1 { fill: #c5c8c6 }
-.terminal-3949666415-r2 { fill: #e3e3e3 }
-.terminal-3949666415-r3 { fill: #989898 }
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-.terminal-3949666415-r10 { fill: #dde6ed;font-weight: bold }
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-.terminal-3949666415-r13 { fill: #454a50 }
-.terminal-3949666415-r14 { fill: #7ae998 }
-.terminal-3949666415-r15 { fill: #e2e3e3;font-weight: bold }
-.terminal-3949666415-r16 { fill: #0a180e;font-weight: bold }
-.terminal-3949666415-r17 { fill: #000000 }
-.terminal-3949666415-r18 { fill: #008139 }
-.terminal-3949666415-r19 { fill: #fea62b;font-weight: bold }
-.terminal-3949666415-r20 { fill: #a7a9ab }
-.terminal-3949666415-r21 { fill: #e2e3e3 }
+ .terminal-3873418736-r1 { fill: #c5c8c6 }
+.terminal-3873418736-r2 { fill: #e3e3e3 }
+.terminal-3873418736-r3 { fill: #989898 }
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+.terminal-3873418736-r20 { fill: #a7a9ab }
+.terminal-3873418736-r21 { fill: #e2e3e3 }
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+
-
+
-
+
- nf-core pipelines create
+ nf-core pipelines create
-
-
-
- ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
-
-
-Template features
-
-
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Use a GitHub Create a GitHub Show help
-▊▁▁▁▁▁▁▁▁▎ repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-pipeline.
-
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Add Github CI testsThe pipeline will Show help
-▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-actions for Continuous
-Integration (CI)
-testing
-▃▃
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Use reference genomesThe pipeline will be Show help
-▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-copy of the most
-common reference
-genome files from
-iGenomes
-
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Add Github badgesThe README.md file of Show help
-▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-include GitHub badges
-
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Add configuration The pipeline will Show help
-▊▁▁▁▁▁▁▁▁▎ filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-profiles containing
-custom parameters
-requried to run
-nf-core pipelines at
-different institutions
-
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Use code lintersThe pipeline will Show help
-▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-and CI tests to lint
-your code: pre-commit,
-▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
- Back Continue
-▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-
- d Toggle dark mode q Quit
+
+
+
+ ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
+
+
+Template features
+
+
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Use a GitHub Create a GitHub Show help
+▊▁▁▁▁▁▁▁▁▎ repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+pipeline.
+
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Add Github CI testsThe pipeline will Show help
+▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+actions for Continuous
+Integration (CI)
+testing
+▃▃
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Use reference genomesThe pipeline will be Show help
+▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+copy of the most
+common reference
+genome files from
+iGenomes
+
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Add Github badgesThe README.md file of Show help
+▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+include GitHub badges
+
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Add configuration The pipeline will Show help
+▊▁▁▁▁▁▁▁▁▎ filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+profiles containing
+custom parameters
+requried to run
+nf-core pipelines at
+different institutions
+
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Use code lintersThe pipeline will Show help
+▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+and CI tests to lint
+your code: pre-commit,
+▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ Back Continue
+▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+
+ d Toggle dark mode q Quit a Toggle all
diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg
index eae763718..c18bb31b8 100644
--- a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg
+++ b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg
@@ -19,254 +19,254 @@
font-weight: 700;
}
- .terminal-3985795459-matrix {
+ .terminal-1108014852-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-3985795459-title {
+ .terminal-1108014852-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-3985795459-r1 { fill: #c5c8c6 }
-.terminal-3985795459-r2 { fill: #e3e3e3 }
-.terminal-3985795459-r3 { fill: #989898 }
-.terminal-3985795459-r4 { fill: #e1e1e1 }
-.terminal-3985795459-r5 { fill: #4ebf71;font-weight: bold }
-.terminal-3985795459-r6 { fill: #1e1e1e }
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-.terminal-3985795459-r10 { fill: #dde6ed;font-weight: bold }
-.terminal-3985795459-r11 { fill: #001541 }
-.terminal-3985795459-r12 { fill: #454a50 }
-.terminal-3985795459-r13 { fill: #7ae998 }
-.terminal-3985795459-r14 { fill: #e2e3e3;font-weight: bold }
-.terminal-3985795459-r15 { fill: #0a180e;font-weight: bold }
-.terminal-3985795459-r16 { fill: #000000 }
-.terminal-3985795459-r17 { fill: #008139 }
-.terminal-3985795459-r18 { fill: #fea62b;font-weight: bold }
-.terminal-3985795459-r19 { fill: #a7a9ab }
-.terminal-3985795459-r20 { fill: #e2e3e3 }
+ .terminal-1108014852-r1 { fill: #c5c8c6 }
+.terminal-1108014852-r2 { fill: #e3e3e3 }
+.terminal-1108014852-r3 { fill: #989898 }
+.terminal-1108014852-r4 { fill: #e1e1e1 }
+.terminal-1108014852-r5 { fill: #4ebf71;font-weight: bold }
+.terminal-1108014852-r6 { fill: #1e1e1e }
+.terminal-1108014852-r7 { fill: #507bb3 }
+.terminal-1108014852-r8 { fill: #e2e2e2 }
+.terminal-1108014852-r9 { fill: #808080 }
+.terminal-1108014852-r10 { fill: #dde6ed;font-weight: bold }
+.terminal-1108014852-r11 { fill: #001541 }
+.terminal-1108014852-r12 { fill: #454a50 }
+.terminal-1108014852-r13 { fill: #7ae998 }
+.terminal-1108014852-r14 { fill: #e2e3e3;font-weight: bold }
+.terminal-1108014852-r15 { fill: #0a180e;font-weight: bold }
+.terminal-1108014852-r16 { fill: #000000 }
+.terminal-1108014852-r17 { fill: #008139 }
+.terminal-1108014852-r18 { fill: #fea62b;font-weight: bold }
+.terminal-1108014852-r19 { fill: #a7a9ab }
+.terminal-1108014852-r20 { fill: #e2e3e3 }
-
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+
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+
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+
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+
-
+
- nf-core pipelines create
+ nf-core pipelines create
-
-
-
- ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
-
-
-Template features
-
-
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Use reference genomesThe pipeline will be Show help
-▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-copy of the most common
-reference genome files
-from iGenomes
-
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Use multiqcThe pipeline will Show help
-▊▁▁▁▁▁▁▁▁▎include the MultiQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-module which generates
-an HTML report for
-quality control.
-
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Use fastqcThe pipeline will Show help
-▊▁▁▁▁▁▁▁▁▎include the FastQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-module which performs
-quality control
-analysis of input FASTQ
-files.
-
-▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
-▊▎ Use nf-schemaUse the nf-schema Show help
-▊▁▁▁▁▁▁▁▁▎Nextflow plugin for ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-this pipeline.
-
-
-
-
-
-
-
-
-
-
-
-
-
-▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
- Back Continue
-▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-
- d Toggle dark mode q Quit
+
+
+
+ ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
+
+
+Template features
+
+
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Use reference genomesThe pipeline will be Show help
+▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+copy of the most common
+reference genome files
+from iGenomes
+
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Use multiqcThe pipeline will Show help
+▊▁▁▁▁▁▁▁▁▎include the MultiQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+module which generates
+an HTML report for
+quality control.
+
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Use fastqcThe pipeline will Show help
+▊▁▁▁▁▁▁▁▁▎include the FastQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+module which performs
+quality control
+analysis of input FASTQ
+files.
+
+▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+▊▎ Use nf-schemaUse the nf-schema Show help
+▊▁▁▁▁▁▁▁▁▎Nextflow plugin for ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+this pipeline.
+
+
+
+
+
+
+
+
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+
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+
+▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ Back Continue
+▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+
+ d Toggle dark mode q Quit a Toggle all
diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg
index 2253bd9ab..fd6f2532c 100644
--- a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg
+++ b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg
@@ -19,255 +19,255 @@
font-weight: 700;
}
- .terminal-3773691015-matrix {
+ .terminal-3655041559-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-3773691015-title {
+ .terminal-3655041559-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-3773691015-r1 { fill: #c5c8c6 }
-.terminal-3773691015-r2 { fill: #e3e3e3 }
-.terminal-3773691015-r3 { fill: #989898 }
-.terminal-3773691015-r4 { fill: #e1e1e1 }
-.terminal-3773691015-r5 { fill: #4ebf71;font-weight: bold }
-.terminal-3773691015-r6 { fill: #a5a5a5;font-style: italic; }
-.terminal-3773691015-r7 { fill: #1e1e1e }
-.terminal-3773691015-r8 { fill: #0f4e2a }
-.terminal-3773691015-r9 { fill: #7b3042 }
-.terminal-3773691015-r10 { fill: #a7a7a7 }
-.terminal-3773691015-r11 { fill: #787878 }
-.terminal-3773691015-r12 { fill: #e2e2e2 }
-.terminal-3773691015-r13 { fill: #b93c5b }
-.terminal-3773691015-r14 { fill: #454a50 }
-.terminal-3773691015-r15 { fill: #7ae998 }
-.terminal-3773691015-r16 { fill: #e2e3e3;font-weight: bold }
-.terminal-3773691015-r17 { fill: #000000 }
-.terminal-3773691015-r18 { fill: #008139 }
-.terminal-3773691015-r19 { fill: #fea62b;font-weight: bold }
-.terminal-3773691015-r20 { fill: #a7a9ab }
-.terminal-3773691015-r21 { fill: #e2e3e3 }
+ .terminal-3655041559-r1 { fill: #c5c8c6 }
+.terminal-3655041559-r2 { fill: #e3e3e3 }
+.terminal-3655041559-r3 { fill: #989898 }
+.terminal-3655041559-r4 { fill: #e1e1e1 }
+.terminal-3655041559-r5 { fill: #4ebf71;font-weight: bold }
+.terminal-3655041559-r6 { fill: #a5a5a5;font-style: italic; }
+.terminal-3655041559-r7 { fill: #1e1e1e }
+.terminal-3655041559-r8 { fill: #0f4e2a }
+.terminal-3655041559-r9 { fill: #7b3042 }
+.terminal-3655041559-r10 { fill: #a7a7a7 }
+.terminal-3655041559-r11 { fill: #787878 }
+.terminal-3655041559-r12 { fill: #e2e2e2 }
+.terminal-3655041559-r13 { fill: #b93c5b }
+.terminal-3655041559-r14 { fill: #454a50 }
+.terminal-3655041559-r15 { fill: #7ae998 }
+.terminal-3655041559-r16 { fill: #e2e3e3;font-weight: bold }
+.terminal-3655041559-r17 { fill: #000000 }
+.terminal-3655041559-r18 { fill: #008139 }
+.terminal-3655041559-r19 { fill: #fea62b;font-weight: bold }
+.terminal-3655041559-r20 { fill: #a7a9ab }
+.terminal-3655041559-r21 { fill: #e2e3e3 }
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+
- nf-core pipelines create
+ nf-core pipelines create
-
-
-
- ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
-
-
-Basic details
-
-
-
-
-GitHub organisationWorkflow name
-
-▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎
-▊nf-core ▎▊Pipeline Name▎
-▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
-Value error, Must be lowercase without
-punctuation.
-
-
-
-A short description of your pipeline.
-
-▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎
-▊Description▎
-▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
-Value error, Cannot be left empty.
-
-
-
-Name of the main author / authors
-
-▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎
-▊Author(s)▎
-▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
-Value error, Cannot be left empty.
-
-▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
- Back Next
-▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
-
-
-
-
-
-
-
-
-
-
-
-
- d Toggle dark mode q Quit
+
+
+
+ ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
+
+
+Basic details
+
+
+
+
+GitHub organisationWorkflow name
+
+▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎
+▊nf-core ▎▊Pipeline Name▎
+▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
+Value error, Must be lowercase without
+punctuation.
+
+
+
+A short description of your pipeline.
+
+▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎
+▊Description▎
+▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
+Value error, Cannot be left empty.
+
+
+
+Name of the main author / authors
+
+▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎
+▊Author(s)▎
+▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎
+Value error, Cannot be left empty.
+
+▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ Back Next
+▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
+
+
+
+
+
+
+
+
+
+
+
+
+ d Toggle dark mode q Quit a Toggle all
diff --git a/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg b/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg
index af00bd0b7..d9941b650 100644
--- a/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg
+++ b/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg
@@ -19,253 +19,253 @@
font-weight: 700;
}
- .terminal-3664377378-matrix {
+ .terminal-2299823026-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-3664377378-title {
+ .terminal-2299823026-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-3664377378-r1 { fill: #c5c8c6 }
-.terminal-3664377378-r2 { fill: #e3e3e3 }
-.terminal-3664377378-r3 { fill: #989898 }
-.terminal-3664377378-r4 { fill: #98e024 }
-.terminal-3664377378-r5 { fill: #626262 }
-.terminal-3664377378-r6 { fill: #9d65ff }
-.terminal-3664377378-r7 { fill: #fd971f }
-.terminal-3664377378-r8 { fill: #e1e1e1 }
-.terminal-3664377378-r9 { fill: #4ebf71;font-weight: bold }
-.terminal-3664377378-r10 { fill: #e1e1e1;text-decoration: underline; }
-.terminal-3664377378-r11 { fill: #18954b }
-.terminal-3664377378-r12 { fill: #e2e2e2 }
-.terminal-3664377378-r13 { fill: #e2e2e2;text-decoration: underline; }
-.terminal-3664377378-r14 { fill: #e2e2e2;font-weight: bold;font-style: italic; }
-.terminal-3664377378-r15 { fill: #7ae998 }
-.terminal-3664377378-r16 { fill: #008139 }
-.terminal-3664377378-r17 { fill: #fea62b;font-weight: bold }
-.terminal-3664377378-r18 { fill: #a7a9ab }
-.terminal-3664377378-r19 { fill: #e2e3e3 }
+ .terminal-2299823026-r1 { fill: #c5c8c6 }
+.terminal-2299823026-r2 { fill: #e3e3e3 }
+.terminal-2299823026-r3 { fill: #989898 }
+.terminal-2299823026-r4 { fill: #98e024 }
+.terminal-2299823026-r5 { fill: #626262 }
+.terminal-2299823026-r6 { fill: #9d65ff }
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- nf-core pipelines create
+ nf-core pipelines create
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- ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
-
-
-Welcome to the nf-core pipeline creation wizard
-
- This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template.
-
- The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core
- pipelines.
-
-▌💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with
-▌the community as early as possible; ideally before you start on your pipeline! See the
-▌nf-core guidelines and the #new-pipelines Slack channel for more information.
-
-
-▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
- Let's go!
-▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
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- d Toggle dark mode q Quit
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+
+
+ ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa…
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+
+
+Welcome to the nf-core pipeline creation wizard
+
+ This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template.
+
+ The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core
+ pipelines.
+
+▌💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with
+▌the community as early as possible; ideally before you start on your pipeline! See the
+▌nf-core guidelines and the #new-pipelines Slack channel for more information.
+
+
+▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔
+ Let's go!
+▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁
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+ d Toggle dark mode q Quit a Toggle all