diff --git a/.github/renovate.json5 b/.github/renovate.json5
index 8d123ab17a..5af6502e95 100644
--- a/.github/renovate.json5
+++ b/.github/renovate.json5
@@ -14,4 +14,5 @@
registryUrls: ["docker.io"],
},
],
+ gitIgnoredAuthors: ["core@nf-co.re"],
}
diff --git a/.github/workflows/changelog.py b/.github/workflows/changelog.py
index eb56499c93..4835b0d0f0 100644
--- a/.github/workflows/changelog.py
+++ b/.github/workflows/changelog.py
@@ -136,12 +136,14 @@ def _skip_existing_entry_for_this_pr(line: str, same_section: bool = True) -> st
# If the line already contains a link to the PR, don't add it again.
line = _skip_existing_entry_for_this_pr(line, same_section=False)
- if line.startswith("# ") and not line.strip() == "# nf-core/tools: Changelog": # Version header, e.g. "# v2.12dev"
+ if (
+ line.startswith("## ") and not line.strip() == "# nf-core/tools: Changelog"
+ ): # Version header, e.g. "## v2.12dev"
print(f"Found version header: {line.strip()}")
updated_lines.append(line)
- # Parse version from the line `# v2.12dev` or
- # `# [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20]` ...
+ # Parse version from the line `## v2.12dev` or
+ # `## [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20]` ...
if not (m := re.match(r".*(v\d+\.\d+(dev)?).*", line)):
print(f"Cannot parse version from line {line.strip()}.", file=sys.stderr)
sys.exit(1)
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 595fff66ae..95a03c70fe 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -10,7 +10,7 @@ jobs:
contains(github.event.comment.html_url, '/pull/') &&
contains(github.event.comment.body, '@nf-core-bot fix linting') &&
github.repository == 'nf-core/tools'
- runs-on: self-hosted
+ runs-on: ubuntu-latest
steps:
# Use the @nf-core-bot token to check out so we can push later
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 8a4afe9161..12c8a34000 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -195,7 +195,7 @@ jobs:
coverage report
coverage xml
- - uses: codecov/codecov-action@v3
+ - uses: codecov/codecov-action@f30e4959ba63075080d4f7f90cacc18d9f3fafd7 # v4
with:
files: coverage.xml
env:
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index d4eb6a721d..1fdda4978a 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
repos:
- repo: https://github.com/astral-sh/ruff-pre-commit
- rev: v0.1.14
+ rev: v0.1.15
hooks:
- id: ruff # linter
args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4ec71a8282..70cf2de07a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,22 @@
# nf-core/tools: Changelog
-# [v2.12 - Aluminium Wolf](https://github.com/nf-core/tools/releases/tag/2.11) - [2024-01-29]
+## [v2.12.1 - Aluminium Wolf - Patch](https://github.com/nf-core/tools/releases/tag/2.12.1) - [2024-02-01]
+
+### Linting
+
+- Handle default values of type number from nextflow schema ([#2703](https://github.com/nf-core/tools/pull/2703))
+- fix ignoring files_unchanged ([#2707](https://github.com/nf-core/tools/pull/2707))
+
+### General
+
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.1.15 ([#2705](https://github.com/nf-core/tools/pull/2705))
+- use types for default value comparison ([#2712](https://github.com/nf-core/tools/pull/2712))
+- fix changelog titles ([#2708](https://github.com/nf-core/tools/pull/2708))
+- Print relative path not absolute path in logo cmd log output ([#2709](https://github.com/nf-core/tools/pull/2709))
+- Update codecov/codecov-action action to v4 ([#2713](https://github.com/nf-core/tools/pull/2713))
+- Ignore nf-core-bot in renovate PRs ([#2716](https://github.com/nf-core/tools/pull/2716))
+
+## [v2.12 - Aluminium Wolf](https://github.com/nf-core/tools/releases/tag/2.12) - [2024-01-29]
### Template
@@ -46,7 +62,7 @@
- Update peter-evans/create-or-update-comment action to v4 ([#2683](https://github.com/nf-core/tools/pull/2683))
- Update peter-evans/create-or-update-comment action to v4 ([#2695](https://github.com/nf-core/tools/pull/2695))
-# [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20]
+## [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20]
### Template
@@ -57,7 +73,7 @@
- Only dump `modules.json` when it is modified ([#2609](https://github.com/nf-core/tools/pull/2609))
-# [v2.11 - Magnesium Dragon](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-19]
+## [v2.11 - Magnesium Dragon](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-19]
### Template
@@ -113,7 +129,7 @@
- Sort the `installed_by` list in `modules.json` ([#2570](https://github.com/nf-core/tools/pull/2570)).
- Unset env variable JAVA_TOOL_OPTIONS in gitpod ([#2569](https://github.com/nf-core/tools/pull/2569))
-# [v2.10 - Nickel Ostrich](https://github.com/nf-core/tools/releases/tag/2.10) + [2023-09-25]
+## [v2.10 - Nickel Ostrich](https://github.com/nf-core/tools/releases/tag/2.10) + [2023-09-25]
### Template
@@ -157,7 +173,7 @@
- Throw warning when custom workflow name contains special characters ([#2401](https://github.com/nf-core/tools/pull/2401))
- Bump version of nf-test snapshot files with `nf-core bump-version` ([#2410](https://github.com/nf-core/tools/pull/2410))
-# [v2.9 - Chromium Falcon](https://github.com/nf-core/tools/releases/tag/2.9) + [2023-06-29]
+## [v2.9 - Chromium Falcon](https://github.com/nf-core/tools/releases/tag/2.9) + [2023-06-29]
### Template
@@ -225,7 +241,7 @@ _In addition, `-r` / `--revision` has been changed to a parameter that can be pr
- Refgenie: Create `nxf_home/nf-core/refgenie_genomes.config` path if it doesn't exist ([#2312](https://github.com/nf-core/tools/pull/2312))
- Add CI tests to test running a pipeline whe it's created from a template skipping different areas
-# [v2.8 - Ruthenium Monkey](https://github.com/nf-core/tools/releases/tag/2.8) - [2023-04-27]
+## [v2.8 - Ruthenium Monkey](https://github.com/nf-core/tools/releases/tag/2.8) - [2023-04-27]
### Template
diff --git a/docs/images/nf-core-bump-version.svg b/docs/images/nf-core-bump-version.svg
index 602b18304d..af75211d65 100644
--- a/docs/images/nf-core-bump-version.svg
+++ b/docs/images/nf-core-bump-version.svg
@@ -19,122 +19,122 @@
font-weight: 700;
}
- .terminal-760177622-matrix {
+ .terminal-3212272693-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-760177622-title {
+ .terminal-3212272693-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-760177622-r1 { fill: #c5c8c6 }
-.terminal-760177622-r2 { fill: #98a84b }
-.terminal-760177622-r3 { fill: #9a9b99 }
-.terminal-760177622-r4 { fill: #608ab1 }
-.terminal-760177622-r5 { fill: #d0b344 }
-.terminal-760177622-r6 { fill: #cc555a }
+ .terminal-3212272693-r1 { fill: #c5c8c6 }
+.terminal-3212272693-r2 { fill: #98a84b }
+.terminal-3212272693-r3 { fill: #9a9b99 }
+.terminal-3212272693-r4 { fill: #608ab1 }
+.terminal-3212272693-r5 { fill: #d0b344 }
+.terminal-3212272693-r6 { fill: #cc555a }
-
+
-
+
-
+
-
+
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-
+
-
+
-
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-
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-
+
-
+
-
+
-
+
-
+
-
+
-
+
@@ -146,41 +146,41 @@
-
+
-
- $ nf-core bump-version 1.1
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
- nf-core/tools version 2.12 - https://nf-co.re
-
-
-INFO Changing version number from '1.0dev' to '1.1'
-INFO Updated version in 'nextflow.config'
- - version = '1.0dev'
- + version = '1.1'
-
-
-INFO Updated version in 'assets/multiqc_config.yml'
- - This report has been generated by the <a
-href="https://github.com/nf-core/nextbigthing/tree/dev" target="_blank">nf-core/nextbigthing</a>
- + This report has been generated by the <a
-href="https://github.com/nf-core/nextbigthing/releases/tag/1.1"
-target="_blank">nf-core/nextbigthing</a>
-
-
-INFO Updated version in 'assets/multiqc_config.yml'
- - <a href="https://nf-co.re/nextbigthing/dev/docs/output"
-target="_blank">documentation</a>.
- + <a href="https://nf-co.re/nextbigthing/1.1/docs/output"
-target="_blank">documentation</a>.
-
-
+
+ $ nf-core bump-version 1.1
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ nf-core/tools version 2.12.1 - https://nf-co.re
+
+
+INFO Changing version number from '1.0dev' to '1.1'
+INFO Updated version in 'nextflow.config'
+ - version = '1.0dev'
+ + version = '1.1'
+
+
+INFO Updated version in 'assets/multiqc_config.yml'
+ - This report has been generated by the <a
+href="https://github.com/nf-core/nextbigthing/tree/dev" target="_blank">nf-core/nextbigthing</a>
+ + This report has been generated by the <a
+href="https://github.com/nf-core/nextbigthing/releases/tag/1.1"
+target="_blank">nf-core/nextbigthing</a>
+
+
+INFO Updated version in 'assets/multiqc_config.yml'
+ - <a href="https://nf-co.re/nextbigthing/dev/docs/output"
+target="_blank">documentation</a>.
+ + <a href="https://nf-co.re/nextbigthing/1.1/docs/output"
+target="_blank">documentation</a>.
+
+
diff --git a/docs/images/nf-core-create-logo.svg b/docs/images/nf-core-create-logo.svg
index b4d88480d9..5f8bf56128 100644
--- a/docs/images/nf-core-create-logo.svg
+++ b/docs/images/nf-core-create-logo.svg
@@ -19,63 +19,62 @@
font-weight: 700;
}
- .terminal-121252375-matrix {
+ .terminal-2549025252-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-121252375-title {
+ .terminal-2549025252-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-121252375-r1 { fill: #c5c8c6 }
-.terminal-121252375-r2 { fill: #98a84b }
-.terminal-121252375-r3 { fill: #9a9b99 }
-.terminal-121252375-r4 { fill: #608ab1 }
-.terminal-121252375-r5 { fill: #d0b344 }
-.terminal-121252375-r6 { fill: #98729f }
-.terminal-121252375-r7 { fill: #ff2c7a }
+ .terminal-2549025252-r1 { fill: #c5c8c6 }
+.terminal-2549025252-r2 { fill: #98a84b }
+.terminal-2549025252-r3 { fill: #9a9b99 }
+.terminal-2549025252-r4 { fill: #608ab1 }
+.terminal-2549025252-r5 { fill: #d0b344 }
+.terminal-2549025252-r6 { fill: #98729f }
-
+
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+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
@@ -87,21 +86,21 @@
-
+
-
- $ nf-core create-logo nextbigthing
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
- nf-core/tools version 2.12 - https://nf-co.re
-
-
-INFO Created logo: /home/runner/work/tools/tools/tmp/nf-core-nextbigthing_logo_light.png
+
+ $ nf-core create-logo nextbigthing
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ nf-core/tools version 2.12.1 - https://nf-co.re
+
+
+INFO Created logo: nf-core-nextbigthing_logo_light.png
diff --git a/docs/images/nf-core-create.svg b/docs/images/nf-core-create.svg
index 79e349f4fc..02d942a7f9 100644
--- a/docs/images/nf-core-create.svg
+++ b/docs/images/nf-core-create.svg
@@ -19,104 +19,104 @@
font-weight: 700;
}
- .terminal-1826411096-matrix {
+ .terminal-4211528375-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-1826411096-title {
+ .terminal-4211528375-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-1826411096-r1 { fill: #c5c8c6 }
-.terminal-1826411096-r2 { fill: #98a84b }
-.terminal-1826411096-r3 { fill: #9a9b99 }
-.terminal-1826411096-r4 { fill: #608ab1 }
-.terminal-1826411096-r5 { fill: #d0b344 }
-.terminal-1826411096-r6 { fill: #98729f }
-.terminal-1826411096-r7 { fill: #ff2c7a }
-.terminal-1826411096-r8 { fill: #98a84b;font-weight: bold }
-.terminal-1826411096-r9 { fill: #1984e9;text-decoration: underline; }
+ .terminal-4211528375-r1 { fill: #c5c8c6 }
+.terminal-4211528375-r2 { fill: #98a84b }
+.terminal-4211528375-r3 { fill: #9a9b99 }
+.terminal-4211528375-r4 { fill: #608ab1 }
+.terminal-4211528375-r5 { fill: #d0b344 }
+.terminal-4211528375-r6 { fill: #98729f }
+.terminal-4211528375-r7 { fill: #ff2c7a }
+.terminal-4211528375-r8 { fill: #98a84b;font-weight: bold }
+.terminal-4211528375-r9 { fill: #1984e9;text-decoration: underline; }
-
+
-
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-
+
@@ -128,34 +128,34 @@
-
+
-
- $ nf-core create -n nextbigthing -d "This pipeline analyses data from the next big omics technique"
--a "Big Steve" --plain
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
- nf-core/tools version 2.12 - https://nf-co.re
-
-
-INFO Creating new nf-core pipeline: 'nf-core/nextbigthing'
-INFO Initialising pipeline git repository
-INFO Done. Remember to add a remote and push to GitHub:
- cd /home/runner/work/tools/tools/tmp/nf-core-nextbigthing
- git remote add origin git@github.com:USERNAME/REPO_NAME.git
- git push --all origin
-INFO This will also push your newly created dev branch and the TEMPLATE branch for syncing.
-INFO !!!!!! IMPORTANT !!!!!!
-
-If you are interested in adding your pipeline to the nf-core community,
-PLEASE COME AND TALK TO US IN THE NF-CORE SLACK BEFORE WRITING ANY CODE!
-
-Please read: https://nf-co.re/developers/adding_pipelines#join-the-community
+
+ $ nf-core create -n nextbigthing -d "This pipeline analyses data from the next big omics technique"
+-a "Big Steve" --plain
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ nf-core/tools version 2.12.1 - https://nf-co.re
+
+
+INFO Creating new nf-core pipeline: 'nf-core/nextbigthing'
+INFO Initialising pipeline git repository
+INFO Done. Remember to add a remote and push to GitHub:
+ cd /home/runner/work/tools/tools/tmp/nf-core-nextbigthing
+ git remote add origin git@github.com:USERNAME/REPO_NAME.git
+ git push --all origin
+INFO This will also push your newly created dev branch and the TEMPLATE branch for syncing.
+INFO !!!!!! IMPORTANT !!!!!!
+
+If you are interested in adding your pipeline to the nf-core community,
+PLEASE COME AND TALK TO US IN THE NF-CORE SLACK BEFORE WRITING ANY CODE!
+
+Please read: https://nf-co.re/developers/adding_pipelines#join-the-community
diff --git a/docs/images/nf-core-download.svg b/docs/images/nf-core-download.svg
index 05b7456fbd..3d306efb25 100644
--- a/docs/images/nf-core-download.svg
+++ b/docs/images/nf-core-download.svg
@@ -19,86 +19,86 @@
font-weight: 700;
}
- .terminal-1937960304-matrix {
+ .terminal-2749558223-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-1937960304-title {
+ .terminal-2749558223-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-1937960304-r1 { fill: #c5c8c6 }
-.terminal-1937960304-r2 { fill: #98a84b }
-.terminal-1937960304-r3 { fill: #9a9b99 }
-.terminal-1937960304-r4 { fill: #608ab1 }
-.terminal-1937960304-r5 { fill: #d0b344 }
-.terminal-1937960304-r6 { fill: #cc555a }
+ .terminal-2749558223-r1 { fill: #c5c8c6 }
+.terminal-2749558223-r2 { fill: #98a84b }
+.terminal-2749558223-r3 { fill: #9a9b99 }
+.terminal-2749558223-r4 { fill: #608ab1 }
+.terminal-2749558223-r5 { fill: #d0b344 }
+.terminal-2749558223-r6 { fill: #cc555a }
-
+
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-
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-
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+
-
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-
+
@@ -110,29 +110,29 @@
-
+
-
- $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -s none -d
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
- nf-core/tools version 2.12 - https://nf-co.re
-
-
-WARNING Could not find GitHub authentication token. Some API requests may fail.
-INFO Saving 'nf-core/rnaseq'
- Pipeline revision: '3.8'
- Use containers: 'none'
- Container library: 'quay.io'
- Output directory: 'nf-core-rnaseq'
- Include default institutional configuration: 'True'
-INFO Downloading centralised configs from GitHub
-INFO Downloading workflow files from GitHub
+
+ $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -s none -d
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ nf-core/tools version 2.12.1 - https://nf-co.re
+
+
+WARNING Could not find GitHub authentication token. Some API requests may fail.
+INFO Saving 'nf-core/rnaseq'
+ Pipeline revision: '3.8'
+ Use containers: 'none'
+ Container library: 'quay.io'
+ Output directory: 'nf-core-rnaseq'
+ Include default institutional configuration: 'True'
+INFO Downloading centralised configs from GitHub
+INFO Downloading workflow files from GitHub
diff --git a/docs/images/nf-core-launch-rnaseq.svg b/docs/images/nf-core-launch-rnaseq.svg
index 8956e15703..42ac222ed3 100644
--- a/docs/images/nf-core-launch-rnaseq.svg
+++ b/docs/images/nf-core-launch-rnaseq.svg
@@ -19,72 +19,72 @@
font-weight: 700;
}
- .terminal-1862905299-matrix {
+ .terminal-3783306802-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-1862905299-title {
+ .terminal-3783306802-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-1862905299-r1 { fill: #c5c8c6 }
-.terminal-1862905299-r2 { fill: #98a84b }
-.terminal-1862905299-r3 { fill: #9a9b99 }
-.terminal-1862905299-r4 { fill: #608ab1 }
-.terminal-1862905299-r5 { fill: #d0b344 }
-.terminal-1862905299-r6 { fill: #c5c8c6;font-weight: bold }
-.terminal-1862905299-r7 { fill: #68a0b3;font-weight: bold }
+ .terminal-3783306802-r1 { fill: #c5c8c6 }
+.terminal-3783306802-r2 { fill: #98a84b }
+.terminal-3783306802-r3 { fill: #9a9b99 }
+.terminal-3783306802-r4 { fill: #608ab1 }
+.terminal-3783306802-r5 { fill: #d0b344 }
+.terminal-3783306802-r6 { fill: #c5c8c6;font-weight: bold }
+.terminal-3783306802-r7 { fill: #68a0b3;font-weight: bold }
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@@ -96,24 +96,24 @@
-
+
-
- $ nf-core launch rnaseq -r 3.8.1
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
- nf-core/tools version 2.12 - https://nf-co.re
-
-
-INFO NOTE: This tool ignores any pipeline parameter defaults overwritten by Nextflow config
- files or profiles
-
-INFO Downloading workflow: nf-core/rnaseq (3.8.1)
+
+ $ nf-core launch rnaseq -r 3.8.1
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ nf-core/tools version 2.12.1 - https://nf-co.re
+
+
+INFO NOTE: This tool ignores any pipeline parameter defaults overwritten by Nextflow config
+ files or profiles
+
+INFO Downloading workflow: nf-core/rnaseq (3.8.1)
diff --git a/docs/images/nf-core-licences.svg b/docs/images/nf-core-licences.svg
index 0512d5c954..e7971f9883 100644
--- a/docs/images/nf-core-licences.svg
+++ b/docs/images/nf-core-licences.svg
@@ -1,4 +1,4 @@
-