diff --git a/docs/images/nf-core-bump-version.svg b/docs/images/nf-core-bump-version.svg
index d63cc442c5..89843856b2 100644
--- a/docs/images/nf-core-bump-version.svg
+++ b/docs/images/nf-core-bump-version.svg
@@ -19,77 +19,77 @@
font-weight: 700;
}
- .terminal-2897532537-matrix {
+ .terminal-2980173434-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-2897532537-title {
+ .terminal-2980173434-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-2897532537-r1 { fill: #c5c8c6 }
-.terminal-2897532537-r2 { fill: #98a84b }
-.terminal-2897532537-r3 { fill: #9a9b99 }
-.terminal-2897532537-r4 { fill: #608ab1 }
-.terminal-2897532537-r5 { fill: #d0b344 }
-.terminal-2897532537-r6 { fill: #cc555a }
+ .terminal-2980173434-r1 { fill: #c5c8c6 }
+.terminal-2980173434-r2 { fill: #98a84b }
+.terminal-2980173434-r3 { fill: #9a9b99 }
+.terminal-2980173434-r4 { fill: #608ab1 }
+.terminal-2980173434-r5 { fill: #d0b344 }
+.terminal-2980173434-r6 { fill: #cc555a }
-
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+
@@ -101,26 +101,26 @@
-
+
-
- $ nf-core bump-version 1.1
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
- nf-core/tools version 2.7.1 - 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'
-
-
+
+ $ nf-core bump-version 1.1
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ nf-core/tools version 2.7.2 - 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'
+
+
diff --git a/docs/images/nf-core-create.svg b/docs/images/nf-core-create.svg
index 78343c2d34..17b28b0b67 100644
--- a/docs/images/nf-core-create.svg
+++ b/docs/images/nf-core-create.svg
@@ -19,104 +19,104 @@
font-weight: 700;
}
- .terminal-3886862987-matrix {
+ .terminal-4135113356-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-3886862987-title {
+ .terminal-4135113356-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-3886862987-r1 { fill: #c5c8c6 }
-.terminal-3886862987-r2 { fill: #98a84b }
-.terminal-3886862987-r3 { fill: #9a9b99 }
-.terminal-3886862987-r4 { fill: #608ab1 }
-.terminal-3886862987-r5 { fill: #d0b344 }
-.terminal-3886862987-r6 { fill: #98729f }
-.terminal-3886862987-r7 { fill: #ff2c7a }
-.terminal-3886862987-r8 { fill: #98a84b;font-weight: bold }
-.terminal-3886862987-r9 { fill: #1984e9;text-decoration: underline; }
+ .terminal-4135113356-r1 { fill: #c5c8c6 }
+.terminal-4135113356-r2 { fill: #98a84b }
+.terminal-4135113356-r3 { fill: #9a9b99 }
+.terminal-4135113356-r4 { fill: #608ab1 }
+.terminal-4135113356-r5 { fill: #d0b344 }
+.terminal-4135113356-r6 { fill: #98729f }
+.terminal-4135113356-r7 { fill: #ff2c7a }
+.terminal-4135113356-r8 { fill: #98a84b;font-weight: bold }
+.terminal-4135113356-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 2.7.1 - 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
+
+ $ nf-core create -n nextbigthing -d "This pipeline analyses data from the next big omics technique"
+-a "Big Steve" --plain
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ nf-core/tools version 2.7.2 - 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 4db5b62de9..d26c6011d5 100644
--- a/docs/images/nf-core-download.svg
+++ b/docs/images/nf-core-download.svg
@@ -19,76 +19,76 @@
font-weight: 700;
}
- .terminal-405352606-matrix {
+ .terminal-512307359-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-405352606-title {
+ .terminal-512307359-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-405352606-r1 { fill: #c5c8c6 }
-.terminal-405352606-r2 { fill: #98a84b }
-.terminal-405352606-r3 { fill: #9a9b99 }
-.terminal-405352606-r4 { fill: #608ab1 }
-.terminal-405352606-r5 { fill: #d0b344 }
+ .terminal-512307359-r1 { fill: #c5c8c6 }
+.terminal-512307359-r2 { fill: #98a84b }
+.terminal-512307359-r3 { fill: #9a9b99 }
+.terminal-512307359-r4 { fill: #608ab1 }
+.terminal-512307359-r5 { fill: #d0b344 }
-
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+
@@ -100,26 +100,26 @@
-
+
-
- $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -c none
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
- nf-core/tools version 2.7.1 - https://nf-co.re
-
-
-INFO Saving 'nf-core/rnaseq'
- Pipeline revision: '3.8'
- Pull containers: 'none'
- Output directory: 'nf-core-rnaseq'
-INFO Downloading workflow files from GitHub
-INFO Downloading centralised configs from GitHub
+
+ $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -c none
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ nf-core/tools version 2.7.2 - https://nf-co.re
+
+
+INFO Saving 'nf-core/rnaseq'
+ Pipeline revision: '3.8'
+ Pull containers: 'none'
+ Output directory: 'nf-core-rnaseq'
+INFO Downloading workflow files from GitHub
+INFO Downloading centralised configs from GitHub
diff --git a/docs/images/nf-core-launch-rnaseq.svg b/docs/images/nf-core-launch-rnaseq.svg
index 52cfc344e2..c36c892e5a 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-3090263558-matrix {
+ .terminal-3166875143-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-3090263558-title {
+ .terminal-3166875143-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-3090263558-r1 { fill: #c5c8c6 }
-.terminal-3090263558-r2 { fill: #98a84b }
-.terminal-3090263558-r3 { fill: #9a9b99 }
-.terminal-3090263558-r4 { fill: #608ab1 }
-.terminal-3090263558-r5 { fill: #d0b344 }
-.terminal-3090263558-r6 { fill: #c5c8c6;font-weight: bold }
-.terminal-3090263558-r7 { fill: #68a0b3;font-weight: bold }
+ .terminal-3166875143-r1 { fill: #c5c8c6 }
+.terminal-3166875143-r2 { fill: #98a84b }
+.terminal-3166875143-r3 { fill: #9a9b99 }
+.terminal-3166875143-r4 { fill: #608ab1 }
+.terminal-3166875143-r5 { fill: #d0b344 }
+.terminal-3166875143-r6 { fill: #c5c8c6;font-weight: bold }
+.terminal-3166875143-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 2.7.1 - 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)
+
+ $ nf-core launch rnaseq -r 3.8.1
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ nf-core/tools version 2.7.2 - 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 38d2266df9..f96e135487 100644
--- a/docs/images/nf-core-licences.svg
+++ b/docs/images/nf-core-licences.svg
@@ -19,108 +19,108 @@
font-weight: 700;
}
- .terminal-3614362229-matrix {
+ .terminal-3773418102-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-3614362229-title {
+ .terminal-3773418102-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-3614362229-r1 { fill: #c5c8c6 }
-.terminal-3614362229-r2 { fill: #98a84b }
-.terminal-3614362229-r3 { fill: #9a9b99 }
-.terminal-3614362229-r4 { fill: #608ab1 }
-.terminal-3614362229-r5 { fill: #d0b344 }
-.terminal-3614362229-r6 { fill: #68a0b3;font-weight: bold }
-.terminal-3614362229-r7 { fill: #c5c8c6;font-weight: bold }
+ .terminal-3773418102-r1 { fill: #c5c8c6 }
+.terminal-3773418102-r2 { fill: #98a84b }
+.terminal-3773418102-r3 { fill: #9a9b99 }
+.terminal-3773418102-r4 { fill: #608ab1 }
+.terminal-3773418102-r5 { fill: #d0b344 }
+.terminal-3773418102-r6 { fill: #68a0b3;font-weight: bold }
+.terminal-3773418102-r7 { fill: #c5c8c6;font-weight: bold }
-
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-
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-
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-
+
@@ -132,36 +132,36 @@
-
+
-
- $ nf-core licences deepvariant
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
- nf-core/tools version 2.7.1 - https://nf-co.re
-
-
-INFO Fetching licence information for 8 tools
-INFO Warning: This tool only prints licence information for the software tools packaged using
- conda.
-INFO The pipeline may use other software and dependencies not described here.
-โโโโโโโโโโโโโโโโณโโโโโโโโโโณโโโโโโโโโโ
-โPackage NameโVersionโLicenceโ
-โกโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโฉ
-โ lbzip2 โ 2.5 โ GPL v3 โ
-โ deepvariant โ 0.7.0 โ MIT โ
-โ htslib โ 1.9 โ MIT โ
-โ picard โ 2.18.7 โ MIT โ
-โ pip โ 10.0.1 โ MIT โ
-โ samtools โ 1.9 โ MIT โ
-โ python โ 2.7.15 โ PSF โ
-โ bzip2 โ 1.0.6 โ bzip2 โ
-โโโโโโโโโโโโโโโโดโโโโโโโโโโดโโโโโโโโโโ
+
+ $ nf-core licences deepvariant
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ nf-core/tools version 2.7.2 - https://nf-co.re
+
+
+INFO Fetching licence information for 8 tools
+INFO Warning: This tool only prints licence information for the software tools packaged using
+ conda.
+INFO The pipeline may use other software and dependencies not described here.
+โโโโโโโโโโโโโโโโณโโโโโโโโโโณโโโโโโโโโโ
+โPackage NameโVersionโLicenceโ
+โกโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโฉ
+โ lbzip2 โ 2.5 โ GPL v3 โ
+โ deepvariant โ 0.7.0 โ MIT โ
+โ htslib โ 1.9 โ MIT โ
+โ picard โ 2.18.7 โ MIT โ
+โ pip โ 10.0.1 โ MIT โ
+โ samtools โ 1.9 โ MIT โ
+โ python โ 2.7.15 โ PSF โ
+โ bzip2 โ 1.0.6 โ bzip2 โ
+โโโโโโโโโโโโโโโโดโโโโโโโโโโดโโโโโโโโโโ
diff --git a/docs/images/nf-core-lint.svg b/docs/images/nf-core-lint.svg
index 6ba942292b..d375ae1f11 100644
--- a/docs/images/nf-core-lint.svg
+++ b/docs/images/nf-core-lint.svg
@@ -1,4 +1,4 @@
-