diff --git a/docs/images/nf-core-bump-version.svg b/docs/images/nf-core-bump-version.svg
index 528ca47408..c57af953e3 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-541877205-matrix {
+ .terminal-2993841204-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-541877205-title {
+ .terminal-2993841204-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-541877205-r1 { fill: #c5c8c6 }
-.terminal-541877205-r2 { fill: #98a84b }
-.terminal-541877205-r3 { fill: #9a9b99 }
-.terminal-541877205-r4 { fill: #608ab1 }
-.terminal-541877205-r5 { fill: #d0b344 }
-.terminal-541877205-r6 { fill: #cc555a }
+ .terminal-2993841204-r1 { fill: #c5c8c6 }
+.terminal-2993841204-r2 { fill: #98a84b }
+.terminal-2993841204-r3 { fill: #9a9b99 }
+.terminal-2993841204-r4 { fill: #608ab1 }
+.terminal-2993841204-r5 { fill: #d0b344 }
+.terminal-2993841204-r6 { fill: #cc555a }
-
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-
+
-
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-
+
@@ -146,41 +146,41 @@
-
+
-
- $ nf-core bump-version 1.1
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
- nf-core/tools version 2.11 - 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 2.11.1 - 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.svg b/docs/images/nf-core-create.svg
index 680fbe8ad2..99a7112fb4 100644
--- a/docs/images/nf-core-create.svg
+++ b/docs/images/nf-core-create.svg
@@ -19,104 +19,104 @@
font-weight: 700;
}
- .terminal-1578160727-matrix {
+ .terminal-3963146934-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-1578160727-title {
+ .terminal-3963146934-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-1578160727-r1 { fill: #c5c8c6 }
-.terminal-1578160727-r2 { fill: #98a84b }
-.terminal-1578160727-r3 { fill: #9a9b99 }
-.terminal-1578160727-r4 { fill: #608ab1 }
-.terminal-1578160727-r5 { fill: #d0b344 }
-.terminal-1578160727-r6 { fill: #98729f }
-.terminal-1578160727-r7 { fill: #ff2c7a }
-.terminal-1578160727-r8 { fill: #98a84b;font-weight: bold }
-.terminal-1578160727-r9 { fill: #1984e9;text-decoration: underline; }
+ .terminal-3963146934-r1 { fill: #c5c8c6 }
+.terminal-3963146934-r2 { fill: #98a84b }
+.terminal-3963146934-r3 { fill: #9a9b99 }
+.terminal-3963146934-r4 { fill: #608ab1 }
+.terminal-3963146934-r5 { fill: #d0b344 }
+.terminal-3963146934-r6 { fill: #98729f }
+.terminal-3963146934-r7 { fill: #ff2c7a }
+.terminal-3963146934-r8 { fill: #98a84b;font-weight: bold }
+.terminal-3963146934-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 2.11 - 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 2.11.1 - 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 0a327fbaa7..cc6b17ebfd 100644
--- a/docs/images/nf-core-download.svg
+++ b/docs/images/nf-core-download.svg
@@ -19,86 +19,86 @@
font-weight: 700;
}
- .terminal-1787882863-matrix {
+ .terminal-2599349710-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-1787882863-title {
+ .terminal-2599349710-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-1787882863-r1 { fill: #c5c8c6 }
-.terminal-1787882863-r2 { fill: #98a84b }
-.terminal-1787882863-r3 { fill: #9a9b99 }
-.terminal-1787882863-r4 { fill: #608ab1 }
-.terminal-1787882863-r5 { fill: #d0b344 }
-.terminal-1787882863-r6 { fill: #cc555a }
+ .terminal-2599349710-r1 { fill: #c5c8c6 }
+.terminal-2599349710-r2 { fill: #98a84b }
+.terminal-2599349710-r3 { fill: #9a9b99 }
+.terminal-2599349710-r4 { fill: #608ab1 }
+.terminal-2599349710-r5 { fill: #d0b344 }
+.terminal-2599349710-r6 { fill: #cc555a }
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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 2.11 - 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 2.11.1 - 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 53f80a26be..b76e4893c5 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-1786293714-matrix {
+ .terminal-3706564145-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-1786293714-title {
+ .terminal-3706564145-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-1786293714-r1 { fill: #c5c8c6 }
-.terminal-1786293714-r2 { fill: #98a84b }
-.terminal-1786293714-r3 { fill: #9a9b99 }
-.terminal-1786293714-r4 { fill: #608ab1 }
-.terminal-1786293714-r5 { fill: #d0b344 }
-.terminal-1786293714-r6 { fill: #c5c8c6;font-weight: bold }
-.terminal-1786293714-r7 { fill: #68a0b3;font-weight: bold }
+ .terminal-3706564145-r1 { fill: #c5c8c6 }
+.terminal-3706564145-r2 { fill: #98a84b }
+.terminal-3706564145-r3 { fill: #9a9b99 }
+.terminal-3706564145-r4 { fill: #608ab1 }
+.terminal-3706564145-r5 { fill: #d0b344 }
+.terminal-3706564145-r6 { fill: #c5c8c6;font-weight: bold }
+.terminal-3706564145-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 2.11 - 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 2.11.1 - 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 885973ea4a..934458cf62 100644
--- a/docs/images/nf-core-licences.svg
+++ b/docs/images/nf-core-licences.svg
@@ -19,108 +19,108 @@
font-weight: 700;
}
- .terminal-2300693057-matrix {
+ .terminal-3498363552-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-2300693057-title {
+ .terminal-3498363552-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-2300693057-r1 { fill: #c5c8c6 }
-.terminal-2300693057-r2 { fill: #98a84b }
-.terminal-2300693057-r3 { fill: #9a9b99 }
-.terminal-2300693057-r4 { fill: #608ab1 }
-.terminal-2300693057-r5 { fill: #d0b344 }
-.terminal-2300693057-r6 { fill: #68a0b3;font-weight: bold }
-.terminal-2300693057-r7 { fill: #c5c8c6;font-weight: bold }
+ .terminal-3498363552-r1 { fill: #c5c8c6 }
+.terminal-3498363552-r2 { fill: #98a84b }
+.terminal-3498363552-r3 { fill: #9a9b99 }
+.terminal-3498363552-r4 { fill: #608ab1 }
+.terminal-3498363552-r5 { fill: #d0b344 }
+.terminal-3498363552-r6 { fill: #68a0b3;font-weight: bold }
+.terminal-3498363552-r7 { fill: #c5c8c6;font-weight: bold }
-
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+
@@ -132,36 +132,36 @@
-
+
-
- $ nf-core licences deepvariant
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
- nf-core/tools version 2.11 - 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.
-┏━━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┓
-┃Package Name┃Version┃Licence┃
-┡━━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━┩
-│ lbzip2 │ 2.5 │ GPL v3 │
-│ deepvariant │ 0.7.0 │ MIT │
-│ htslib │ 1.9 │ MIT │
-│ picard │ 2.18.7 │ MIT │
-│ pip │ 10.0.1 │ MIT │
-│ samtools │ 1.9 │ MIT │
-│ python │ 2.7.15 │ PSF │
-│ bzip2 │ 1.0.6 │ bzip2 │
-└──────────────┴─────────┴─────────┘
+
+ $ nf-core licences deepvariant
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ nf-core/tools version 2.11.1 - 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.
+┏━━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┓
+┃Package Name┃Version┃Licence┃
+┡━━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━┩
+│ lbzip2 │ 2.5 │ GPL v3 │
+│ deepvariant │ 0.7.0 │ MIT │
+│ htslib │ 1.9 │ MIT │
+│ picard │ 2.18.7 │ MIT │
+│ pip │ 10.0.1 │ MIT │
+│ samtools │ 1.9 │ MIT │
+│ python │ 2.7.15 │ PSF │
+│ bzip2 │ 1.0.6 │ bzip2 │
+└──────────────┴─────────┴─────────┘
diff --git a/docs/images/nf-core-lint.svg b/docs/images/nf-core-lint.svg
index 84e8b387bc..1c6f1dd1b0 100644
--- a/docs/images/nf-core-lint.svg
+++ b/docs/images/nf-core-lint.svg
@@ -19,136 +19,136 @@
font-weight: 700;
}
- .terminal-2427817567-matrix {
+ .terminal-1032032314-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-2427817567-title {
+ .terminal-1032032314-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-2427817567-r1 { fill: #c5c8c6 }
-.terminal-2427817567-r2 { fill: #98a84b }
-.terminal-2427817567-r3 { fill: #9a9b99 }
-.terminal-2427817567-r4 { fill: #608ab1 }
-.terminal-2427817567-r5 { fill: #d0b344 }
-.terminal-2427817567-r6 { fill: #98729f }
-.terminal-2427817567-r7 { fill: #c5c8c6;font-weight: bold }
-.terminal-2427817567-r8 { fill: #1984e9 }
-.terminal-2427817567-r9 { fill: #d0b344;font-weight: bold }
-.terminal-2427817567-r10 { fill: #fdfdc5 }
-.terminal-2427817567-r11 { fill: #cc555a }
+ .terminal-1032032314-r1 { fill: #c5c8c6 }
+.terminal-1032032314-r2 { fill: #98a84b }
+.terminal-1032032314-r3 { fill: #9a9b99 }
+.terminal-1032032314-r4 { fill: #608ab1 }
+.terminal-1032032314-r5 { fill: #d0b344 }
+.terminal-1032032314-r6 { fill: #98729f }
+.terminal-1032032314-r7 { fill: #c5c8c6;font-weight: bold }
+.terminal-1032032314-r8 { fill: #1984e9 }
+.terminal-1032032314-r9 { fill: #d0b344;font-weight: bold }
+.terminal-1032032314-r10 { fill: #fdfdc5 }
+.terminal-1032032314-r11 { fill: #cc555a }
-
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@@ -160,44 +160,44 @@
-
+
-
- $ nf-core lint
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
- nf-core/tools version 2.11 - https://nf-co.re
-
-
-
-INFO Testing pipeline: .
-
-
-╭─[?] 1 Pipeline Test Ignored────────────────────────────────────────────────────────────────────╮
-││
-│pipeline_todos: pipeline_todos│
-││
-╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
-╭─[!] 1 Pipeline Test Warning────────────────────────────────────────────────────────────────────╮
-││
-│readme: README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo │
-│doi (after the first release).│
-││
-╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
-
-╭──────────────────────╮
-│LINT RESULTS SUMMARY│
-├──────────────────────┤
-│[✔] 192 Tests Passed│
-│[?] 1 Test Ignored│
-│[!] 1 Test Warning│
-│[✗] 0 Tests Failed│
-╰──────────────────────╯
+
+ $ nf-core lint
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ nf-core/tools version 2.11.1 - https://nf-co.re
+
+
+
+INFO Testing pipeline: .
+
+
+╭─[?] 1 Pipeline Test Ignored────────────────────────────────────────────────────────────────────╮
+││
+│pipeline_todos: pipeline_todos│
+││
+╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
+╭─[!] 1 Pipeline Test Warning────────────────────────────────────────────────────────────────────╮
+││
+│readme: README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo │
+│doi (after the first release).│
+││
+╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
+
+╭──────────────────────╮
+│LINT RESULTS SUMMARY│
+├──────────────────────┤
+│[✔] 192 Tests Passed│
+│[?] 1 Test Ignored│
+│[!] 1 Test Warning│
+│[✗] 0 Tests Failed│
+╰──────────────────────╯
diff --git a/docs/images/nf-core-list-rna.svg b/docs/images/nf-core-list-rna.svg
index b5f6ba62c2..ed22bfbc6f 100644
--- a/docs/images/nf-core-list-rna.svg
+++ b/docs/images/nf-core-list-rna.svg
@@ -19,111 +19,111 @@
font-weight: 700;
}
- .terminal-874370221-matrix {
+ .terminal-1199297796-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-874370221-title {
+ .terminal-1199297796-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-874370221-r1 { fill: #c5c8c6 }
-.terminal-874370221-r2 { fill: #98a84b }
-.terminal-874370221-r3 { fill: #9a9b99 }
-.terminal-874370221-r4 { fill: #608ab1 }
-.terminal-874370221-r5 { fill: #d0b344 }
-.terminal-874370221-r6 { fill: #c5c8c6;font-weight: bold }
-.terminal-874370221-r7 { fill: #868887 }
+ .terminal-1199297796-r1 { fill: #c5c8c6 }
+.terminal-1199297796-r2 { fill: #98a84b }
+.terminal-1199297796-r3 { fill: #9a9b99 }
+.terminal-1199297796-r4 { fill: #608ab1 }
+.terminal-1199297796-r5 { fill: #d0b344 }
+.terminal-1199297796-r6 { fill: #c5c8c6;font-weight: bold }
+.terminal-1199297796-r7 { fill: #868887 }
-
+
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-
+
@@ -135,37 +135,37 @@
-
+
-
- $ nf-core list rna rna-seq
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
- nf-core/tools version 2.11 - https://nf-co.re
-
-
-┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓
-┃┃┃┃┃┃Have latest ┃
-┃Pipeline Name ┃Stars┃Latest Release┃ Released┃Last Pulled┃release? ┃
-┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩
-│ rnafusion │ 119 │ 3.0.1 │ 3 weeks ago │ - │ - │
-│ rnaseq │ 704 │ 3.13.2 │ 4 weeks ago │ - │ - │
-│ differentialabundan… │ 32 │ 1.4.0 │ 3 weeks ago │ - │ - │
-│ spatialtranscriptom… │ 31 │ dev │ 3 weeks ago │ - │ - │
-│ circrna │ 33 │ dev │ 3 weeks ago │ - │ - │
-│ rnasplice │ 14 │ 1.0.1 │ 1 months ago │ - │ - │
-│ smrnaseq │ 60 │ 2.2.4 │ 2 months ago │ - │ - │
-│ scrnaseq │ 110 │ 2.4.1 │ 3 months ago │ - │ - │
-│ dualrnaseq │ 13 │ 1.0.0 │ 3 years ago │ - │ - │
-│ marsseq │ 4 │ 1.0.3 │ 5 months ago │ - │ - │
-│ lncpipe │ 26 │ dev │ 1 years ago │ - │ - │
-│ scflow │ 22 │ dev │ 2 years ago │ - │ - │
-└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘
+
+ $ nf-core list rna rna-seq
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ nf-core/tools version 2.11.1 - https://nf-co.re
+
+
+┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓
+┃┃┃┃┃┃Have latest ┃
+┃Pipeline Name ┃Stars┃Latest Release┃ Released┃Last Pulled┃release? ┃
+┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩
+│ rnafusion │ 120 │ 3.0.1 │ 3 weeks ago │ - │ - │
+│ rnaseq │ 704 │ 3.13.2 │ 4 weeks ago │ - │ - │
+│ differentialabundan… │ 32 │ 1.4.0 │ 3 weeks ago │ - │ - │
+│ spatialtranscriptom… │ 31 │ dev │ 3 weeks ago │ - │ - │
+│ circrna │ 33 │ dev │ 3 weeks ago │ - │ - │
+│ rnasplice │ 14 │ 1.0.1 │ 1 months ago │ - │ - │
+│ smrnaseq │ 60 │ 2.2.4 │ 2 months ago │ - │ - │
+│ scrnaseq │ 110 │ 2.4.1 │ 3 months ago │ - │ - │
+│ dualrnaseq │ 13 │ 1.0.0 │ 3 years ago │ - │ - │
+│ marsseq │ 4 │ 1.0.3 │ 5 months ago │ - │ - │
+│ lncpipe │ 26 │ dev │ 1 years ago │ - │ - │
+│ scflow │ 22 │ dev │ 2 years ago │ - │ - │
+└──────────────────────┴───────┴────────────────┴──────────────┴─────────────┴─────────────────────┘
diff --git a/docs/images/nf-core-list-stars.svg b/docs/images/nf-core-list-stars.svg
index 0d741d48ba..01431bf102 100644
--- a/docs/images/nf-core-list-stars.svg
+++ b/docs/images/nf-core-list-stars.svg
@@ -19,88 +19,88 @@
font-weight: 700;
}
- .terminal-2494560554-matrix {
+ .terminal-11073929-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-2494560554-title {
+ .terminal-11073929-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-2494560554-r1 { fill: #c5c8c6 }
-.terminal-2494560554-r2 { fill: #98a84b }
-.terminal-2494560554-r3 { fill: #9a9b99 }
-.terminal-2494560554-r4 { fill: #608ab1 }
-.terminal-2494560554-r5 { fill: #d0b344 }
-.terminal-2494560554-r6 { fill: #c5c8c6;font-weight: bold }
-.terminal-2494560554-r7 { fill: #868887 }
-.terminal-2494560554-r8 { fill: #868887;font-style: italic; }
+ .terminal-11073929-r1 { fill: #c5c8c6 }
+.terminal-11073929-r2 { fill: #98a84b }
+.terminal-11073929-r3 { fill: #9a9b99 }
+.terminal-11073929-r4 { fill: #608ab1 }
+.terminal-11073929-r5 { fill: #d0b344 }
+.terminal-11073929-r6 { fill: #c5c8c6;font-weight: bold }
+.terminal-11073929-r7 { fill: #868887 }
+.terminal-11073929-r8 { fill: #868887;font-style: italic; }
-
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+
@@ -112,29 +112,29 @@
-
+
-
- $ nf-core list -s stars
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
- nf-core/tools version 2.11 - https://nf-co.re
-
-
-┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓
-┃┃┃┃┃┃Have latest ┃
-┃Pipeline Name ┃Stars┃Latest Release┃ Released┃Last Pulled┃release? ┃
-┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩
-│ rnaseq │ 704 │ 3.13.2 │ 4 weeks ago │ - │ - │
-│ sarek │ 288 │ 3.4.0 │ 1 months ago │ - │ - │
-│ chipseq │ 157 │ 2.0.0 │ 1 years ago │ - │ - │
-│ mag │ 156 │ 2.5.1 │ 1 months ago │ - │ - │
-[..truncated..]
+
+ $ nf-core list -s stars
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ nf-core/tools version 2.11.1 - https://nf-co.re
+
+
+┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓
+┃┃┃┃┃┃Have latest ┃
+┃Pipeline Name ┃Stars┃Latest Release┃ Released┃Last Pulled┃release? ┃
+┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩
+│ rnaseq │ 704 │ 3.13.2 │ 4 weeks ago │ - │ - │
+│ sarek │ 288 │ 3.4.0 │ 1 months ago │ - │ - │
+│ chipseq │ 157 │ 2.0.0 │ 1 years ago │ - │ - │
+│ mag │ 156 │ 2.5.1 │ 1 months ago │ - │ - │
+[..truncated..]
diff --git a/docs/images/nf-core-list.svg b/docs/images/nf-core-list.svg
index 2d8873a082..d0b37306a3 100644
--- a/docs/images/nf-core-list.svg
+++ b/docs/images/nf-core-list.svg
@@ -19,91 +19,91 @@
font-weight: 700;
}
- .terminal-1618644398-matrix {
+ .terminal-691768826-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-1618644398-title {
+ .terminal-691768826-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-1618644398-r1 { fill: #c5c8c6 }
-.terminal-1618644398-r2 { fill: #98a84b }
-.terminal-1618644398-r3 { fill: #9a9b99 }
-.terminal-1618644398-r4 { fill: #608ab1 }
-.terminal-1618644398-r5 { fill: #d0b344 }
-.terminal-1618644398-r6 { fill: #c5c8c6;font-weight: bold }
-.terminal-1618644398-r7 { fill: #868887 }
-.terminal-1618644398-r8 { fill: #868887;font-style: italic; }
+ .terminal-691768826-r1 { fill: #c5c8c6 }
+.terminal-691768826-r2 { fill: #98a84b }
+.terminal-691768826-r3 { fill: #9a9b99 }
+.terminal-691768826-r4 { fill: #608ab1 }
+.terminal-691768826-r5 { fill: #d0b344 }
+.terminal-691768826-r6 { fill: #c5c8c6;font-weight: bold }
+.terminal-691768826-r7 { fill: #868887 }
+.terminal-691768826-r8 { fill: #868887;font-style: italic; }
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@@ -115,30 +115,30 @@
-
+
-
- $ nf-core list
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
- nf-core/tools version 2.11 - https://nf-co.re
-
-
-┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓
-┃┃┃┃┃┃Have latest ┃
-┃Pipeline Name ┃Stars┃Latest Release┃ Released┃Last Pulled┃release? ┃
-┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩
-│ ampliseq │ 140 │ 2.7.1 │ 1 months ago │ - │ - │
-│ raredisease │ 63 │ 1.1.1 │ 5 months ago │ - │ - │
-│ epitopeprediction │ 27 │ 2.2.1 │ 9 months ago │ - │ - │
-│ metatdenovo │ 3 │ dev │ 5 hours ago │ - │ - │
-│ metaboigniter │ 11 │ 2.0.0 │ 4 hours ago │ - │ - │
-[..truncated..]
+
+ $ nf-core list
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ nf-core/tools version 2.11.1 - https://nf-co.re
+
+
+┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓
+┃┃┃┃┃┃Have latest ┃
+┃Pipeline Name ┃Stars┃Latest Release┃ Released┃Last Pulled┃release? ┃
+┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩
+│ callingcards │ 2 │ dev │ 18 hours ago │ - │ - │
+│ ampliseq │ 140 │ 2.7.1 │ 1 months ago │ - │ - │
+│ raredisease │ 63 │ 1.1.1 │ 5 months ago │ - │ - │
+│ epitopeprediction │ 27 │ 2.2.1 │ 9 months ago │ - │ - │
+│ metatdenovo │ 3 │ dev │ yesterday │ - │ - │
+[..truncated..]
diff --git a/docs/images/nf-core-modules-bump-version.svg b/docs/images/nf-core-modules-bump-version.svg
index 8ac4ba322d..13be58189e 100644
--- a/docs/images/nf-core-modules-bump-version.svg
+++ b/docs/images/nf-core-modules-bump-version.svg
@@ -19,90 +19,90 @@
font-weight: 700;
}
- .terminal-200931299-matrix {
+ .terminal-1176762434-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-200931299-title {
+ .terminal-1176762434-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-200931299-r1 { fill: #c5c8c6 }
-.terminal-200931299-r2 { fill: #98a84b }
-.terminal-200931299-r3 { fill: #9a9b99 }
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-.terminal-200931299-r6 { fill: #98a84b;font-weight: bold }
-.terminal-200931299-r7 { fill: #c5c8c6;font-weight: bold }
+ .terminal-1176762434-r1 { fill: #c5c8c6 }
+.terminal-1176762434-r2 { fill: #98a84b }
+.terminal-1176762434-r3 { fill: #9a9b99 }
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+.terminal-1176762434-r6 { fill: #98a84b;font-weight: bold }
+.terminal-1176762434-r7 { fill: #c5c8c6;font-weight: bold }
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-
+
-
+
-
+
@@ -114,30 +114,30 @@
-
+
-
- $ nf-core modules bump-versions fastqc
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
- nf-core/tools version 2.11 - https://nf-co.re
-
-
-
-
-╭──────────────────────────────────────────────────────────────────────────────────────────────────╮
-│[!] 1 Module version up to date.│
-╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
-╭──────────────────────────────────────────┬───────────────────────────────────────────────────────╮
-│Module name │Update Message │
-├──────────────────────────────────────────┼───────────────────────────────────────────────────────┤
-│ fastqc │ Module version up to date: fastqc │
-╰──────────────────────────────────────────┴───────────────────────────────────────────────────────╯
+
+ $ nf-core modules bump-versions fastqc
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ nf-core/tools version 2.11.1 - https://nf-co.re
+
+
+
+
+╭──────────────────────────────────────────────────────────────────────────────────────────────────╮
+│[!] 1 Module version up to date.│
+╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
+╭──────────────────────────────────────────┬───────────────────────────────────────────────────────╮
+│Module name │Update Message │
+├──────────────────────────────────────────┼───────────────────────────────────────────────────────┤
+│ fastqc │ Module version up to date: fastqc │
+╰──────────────────────────────────────────┴───────────────────────────────────────────────────────╯
diff --git a/docs/images/nf-core-modules-create.svg b/docs/images/nf-core-modules-create.svg
index 65d9c90131..7cf8b9ca99 100644
--- a/docs/images/nf-core-modules-create.svg
+++ b/docs/images/nf-core-modules-create.svg
@@ -19,104 +19,104 @@
font-weight: 700;
}
- .terminal-95821698-matrix {
+ .terminal-3904970721-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-95821698-title {
+ .terminal-3904970721-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-95821698-r1 { fill: #c5c8c6 }
-.terminal-95821698-r2 { fill: #98a84b }
-.terminal-95821698-r3 { fill: #9a9b99 }
-.terminal-95821698-r4 { fill: #608ab1 }
-.terminal-95821698-r5 { fill: #d0b344 }
-.terminal-95821698-r6 { fill: #68a0b3;font-weight: bold }
+ .terminal-3904970721-r1 { fill: #c5c8c6 }
+.terminal-3904970721-r2 { fill: #98a84b }
+.terminal-3904970721-r3 { fill: #9a9b99 }
+.terminal-3904970721-r4 { fill: #608ab1 }
+.terminal-3904970721-r5 { fill: #d0b344 }
+.terminal-3904970721-r6 { fill: #68a0b3;font-weight: bold }
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+
@@ -128,35 +128,35 @@
-
+
-
- $ nf-core modules create fastqc --author @nf-core-bot --label process_low --meta --force
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
- nf-core/tools version 2.11 - https://nf-co.re
-
-
-
-INFO Repository type: modules
-INFO Press enter to use default values (shown in brackets)or type your own responses.
-ctrl+click underlined text to open links.
-INFO Using Bioconda package: 'bioconda::fastqc=0.12.1'
-INFO Using Docker container: 'biocontainers/fastqc:0.12.1--hdfd78af_0'
-INFO Using Singularity container:
-'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0'
-INFO Created component template: 'fastqc'
-INFO Created following files:
- modules/nf-core/fastqc/main.nf
- modules/nf-core/fastqc/meta.yml
- modules/nf-core/fastqc/environment.yml
- modules/nf-core/fastqc/tests/tags.yml
- modules/nf-core/fastqc/tests/main.nf.test
+
+ $ nf-core modules create fastqc --author @nf-core-bot --label process_low --meta --force
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ nf-core/tools version 2.11.1 - https://nf-co.re
+
+
+
+INFO Repository type: modules
+INFO Press enter to use default values (shown in brackets)or type your own responses.
+ctrl+click underlined text to open links.
+INFO Using Bioconda package: 'bioconda::fastqc=0.12.1'
+INFO Using Docker container: 'biocontainers/fastqc:0.12.1--hdfd78af_0'
+INFO Using Singularity container:
+'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0'
+INFO Created component template: 'fastqc'
+INFO Created following files:
+ modules/nf-core/fastqc/main.nf
+ modules/nf-core/fastqc/meta.yml
+ modules/nf-core/fastqc/environment.yml
+ modules/nf-core/fastqc/tests/tags.yml
+ modules/nf-core/fastqc/tests/main.nf.test
diff --git a/docs/images/nf-core-modules-info.svg b/docs/images/nf-core-modules-info.svg
index ea713ba23c..b604cb3f7b 100644
--- a/docs/images/nf-core-modules-info.svg
+++ b/docs/images/nf-core-modules-info.svg
@@ -19,163 +19,163 @@
font-weight: 700;
}
- .terminal-1933046224-matrix {
+ .terminal-149484079-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-1933046224-title {
+ .terminal-149484079-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-1933046224-r1 { fill: #c5c8c6 }
-.terminal-1933046224-r2 { fill: #98a84b }
-.terminal-1933046224-r3 { fill: #9a9b99 }
-.terminal-1933046224-r4 { fill: #608ab1 }
-.terminal-1933046224-r5 { fill: #d0b344 }
-.terminal-1933046224-r6 { fill: #c5c8c6;font-weight: bold }
-.terminal-1933046224-r7 { fill: #98a84b;font-weight: bold }
-.terminal-1933046224-r8 { fill: #868887 }
-.terminal-1933046224-r9 { fill: #d08442 }
-.terminal-1933046224-r10 { fill: #868887;font-style: italic; }
-.terminal-1933046224-r11 { fill: #98729f }
+ .terminal-149484079-r1 { fill: #c5c8c6 }
+.terminal-149484079-r2 { fill: #98a84b }
+.terminal-149484079-r3 { fill: #9a9b99 }
+.terminal-149484079-r4 { fill: #608ab1 }
+.terminal-149484079-r5 { fill: #d0b344 }
+.terminal-149484079-r6 { fill: #c5c8c6;font-weight: bold }
+.terminal-149484079-r7 { fill: #98a84b;font-weight: bold }
+.terminal-149484079-r8 { fill: #868887 }
+.terminal-149484079-r9 { fill: #d08442 }
+.terminal-149484079-r10 { fill: #868887;font-style: italic; }
+.terminal-149484079-r11 { fill: #98729f }
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@@ -187,53 +187,53 @@
-
+
-
- $ nf-core modules info abacas
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
- nf-core/tools version 2.11 - https://nf-co.re
-
-
-
-╭─ Module: abacas ────────────────────────────────────────────────────────────────────────────────╮
-│ 🌐 Repository: https://github.com/nf-core/modules.git │
-│ 🔧 Tools: abacas │
-│ 📖 Description: contiguate draft genome assembly │
-╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
- ╷ ╷
-📥 Inputs │Description │ Pattern
-╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸
- meta (map) │Groovy Map containing sample information e.g. [ id:'test', │
- │single_end:false ] │
-╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴
- scaffold (file)│Fasta file containing scaffold │*.{fasta,fa}
-╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴
- fasta (file) │FASTA reference file │*.{fasta,fa}
- ╵ ╵
- ╷ ╷
-📤 Outputs │Description │ Pattern
-╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸
- meta (map) │Groovy Map containing sample information e.g. [ id:'test', │
- │single_end:false ] │
-╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴
- results (file) │List containing abacas output files [ 'test.abacas.bin', │ *.{abacas}*
- │'test.abacas.fasta', 'test.abacas.gaps', 'test.abacas.gaps.tab', │
- │'test.abacas.nucmer.delta', 'test.abacas.nucmer.filtered.delta', │
- │'test.abacas.nucmer.tiling', 'test.abacas.tab', │
- │'test.abacas.unused.contigs.out', 'test.abacas.MULTIFASTA.fa' ] │
-╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴
- versions (file)│File containing software versions │versions.yml
- ╵ ╵
-
- 💻 Installation command: nf-core modules install abacas
-
+
+ $ nf-core modules info abacas
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ nf-core/tools version 2.11.1 - https://nf-co.re
+
+
+
+╭─ Module: abacas ────────────────────────────────────────────────────────────────────────────────╮
+│ 🌐 Repository: https://github.com/nf-core/modules.git │
+│ 🔧 Tools: abacas │
+│ 📖 Description: contiguate draft genome assembly │
+╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
+ ╷ ╷
+📥 Inputs │Description │ Pattern
+╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸
+ meta (map) │Groovy Map containing sample information e.g. [ id:'test', │
+ │single_end:false ] │
+╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴
+ scaffold (file)│Fasta file containing scaffold │*.{fasta,fa}
+╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴
+ fasta (file) │FASTA reference file │*.{fasta,fa}
+ ╵ ╵
+ ╷ ╷
+📤 Outputs │Description │ Pattern
+╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸
+ meta (map) │Groovy Map containing sample information e.g. [ id:'test', │
+ │single_end:false ] │
+╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴
+ results (file) │List containing abacas output files [ 'test.abacas.bin', │ *.{abacas}*
+ │'test.abacas.fasta', 'test.abacas.gaps', 'test.abacas.gaps.tab', │
+ │'test.abacas.nucmer.delta', 'test.abacas.nucmer.filtered.delta', │
+ │'test.abacas.nucmer.tiling', 'test.abacas.tab', │
+ │'test.abacas.unused.contigs.out', 'test.abacas.MULTIFASTA.fa' ] │
+╶─────────────────┼───────────────────────────────────────────────────────────────────┼────────────╴
+ versions (file)│File containing software versions │versions.yml
+ ╵ ╵
+
+ 💻 Installation command: nf-core modules install abacas
+
diff --git a/docs/images/nf-core-modules-install.svg b/docs/images/nf-core-modules-install.svg
index 9ebfbce6d7..f444190f32 100644
--- a/docs/images/nf-core-modules-install.svg
+++ b/docs/images/nf-core-modules-install.svg
@@ -19,76 +19,76 @@
font-weight: 700;
}
- .terminal-2637794350-matrix {
+ .terminal-160730253-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-2637794350-title {
+ .terminal-160730253-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-2637794350-r1 { fill: #c5c8c6 }
-.terminal-2637794350-r2 { fill: #98a84b }
-.terminal-2637794350-r3 { fill: #9a9b99 }
-.terminal-2637794350-r4 { fill: #608ab1 }
-.terminal-2637794350-r5 { fill: #d0b344 }
+ .terminal-160730253-r1 { fill: #c5c8c6 }
+.terminal-160730253-r2 { fill: #98a84b }
+.terminal-160730253-r3 { fill: #9a9b99 }
+.terminal-160730253-r4 { fill: #608ab1 }
+.terminal-160730253-r5 { fill: #d0b344 }
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@@ -100,26 +100,26 @@
-
+
-
- $ nf-core modules install abacas
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
- nf-core/tools version 2.11 - https://nf-co.re
-
-
-
-INFO Installing 'abacas'
-INFO Use the following statement to include this module:
-
- include { ABACAS } from '../modules/nf-core/abacas/main'
-
+
+ $ nf-core modules install abacas
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ nf-core/tools version 2.11.1 - https://nf-co.re
+
+
+
+INFO Installing 'abacas'
+INFO Use the following statement to include this module:
+
+ include { ABACAS } from '../modules/nf-core/abacas/main'
+
diff --git a/docs/images/nf-core-modules-lint.svg b/docs/images/nf-core-modules-lint.svg
index 9c364ea5b3..03edcaf551 100644
--- a/docs/images/nf-core-modules-lint.svg
+++ b/docs/images/nf-core-modules-lint.svg
@@ -19,125 +19,125 @@
font-weight: 700;
}
- .terminal-1959956913-matrix {
+ .terminal-3750531600-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-1959956913-title {
+ .terminal-3750531600-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-1959956913-r1 { fill: #c5c8c6 }
-.terminal-1959956913-r2 { fill: #98a84b }
-.terminal-1959956913-r3 { fill: #9a9b99 }
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-.terminal-1959956913-r5 { fill: #d0b344 }
-.terminal-1959956913-r6 { fill: #68a0b3;font-weight: bold }
-.terminal-1959956913-r7 { fill: #d0b344;font-weight: bold }
-.terminal-1959956913-r8 { fill: #8d7b39 }
-.terminal-1959956913-r9 { fill: #fdfdc5 }
-.terminal-1959956913-r10 { fill: #c5c8c6;font-weight: bold }
-.terminal-1959956913-r11 { fill: #98a84b;font-weight: bold }
-.terminal-1959956913-r12 { fill: #cc555a }
+ .terminal-3750531600-r1 { fill: #c5c8c6 }
+.terminal-3750531600-r2 { fill: #98a84b }
+.terminal-3750531600-r3 { fill: #9a9b99 }
+.terminal-3750531600-r4 { fill: #608ab1 }
+.terminal-3750531600-r5 { fill: #d0b344 }
+.terminal-3750531600-r6 { fill: #68a0b3;font-weight: bold }
+.terminal-3750531600-r7 { fill: #d0b344;font-weight: bold }
+.terminal-3750531600-r8 { fill: #8d7b39 }
+.terminal-3750531600-r9 { fill: #fdfdc5 }
+.terminal-3750531600-r10 { fill: #c5c8c6;font-weight: bold }
+.terminal-3750531600-r11 { fill: #98a84b;font-weight: bold }
+.terminal-3750531600-r12 { fill: #cc555a }
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@@ -149,40 +149,40 @@
-
+
-
- $ nf-core modules lint multiqc
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
- nf-core/tools version 2.11 - https://nf-co.re
-
-
-
-INFO Linting modules repo: '.'
-INFO Linting module: 'multiqc'
-INFO Found 4 inputs in modules/nf-core/multiqc/main.nf
-INFO Found 4 outputs in modules/nf-core/multiqc/main.nf
-
-╭─[!] 1 Module Test Warning──────────────────────────────────────────────────────────────────────╮
-│ ╷ ╷ │
-│Module name │File path │Test message │
-│╶─────────────┼─────────────────────────────────┼────────────────────────────────────────────────╴│
-│multiqc│modules/nf-core/multiqc/main.nf│Conda update: bioconda::multiqc 1.18 -> 1.19│
-│ ╵ ╵ │
-╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
-╭──────────────────────╮
-│LINT RESULTS SUMMARY│
-├──────────────────────┤
-│[✔] 50 Tests Passed│
-│[!] 1 Test Warning│
-│[✗] 0 Tests Failed│
-╰──────────────────────╯
+
+ $ nf-core modules lint multiqc
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ nf-core/tools version 2.11.1 - https://nf-co.re
+
+
+
+INFO Linting modules repo: '.'
+INFO Linting module: 'multiqc'
+INFO Found 4 inputs in modules/nf-core/multiqc/main.nf
+INFO Found 4 outputs in modules/nf-core/multiqc/main.nf
+
+╭─[!] 1 Module Test Warning──────────────────────────────────────────────────────────────────────╮
+│ ╷ ╷ │
+│Module name │File path │Test message │
+│╶─────────────┼─────────────────────────────────┼────────────────────────────────────────────────╴│
+│multiqc│modules/nf-core/multiqc/main.nf│Conda update: bioconda::multiqc 1.18 -> 1.19│
+│ ╵ ╵ │
+╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
+╭──────────────────────╮
+│LINT RESULTS SUMMARY│
+├──────────────────────┤
+│[✔] 50 Tests Passed│
+│[!] 1 Test Warning│
+│[✗] 0 Tests Failed│
+╰──────────────────────╯
diff --git a/docs/images/nf-core-modules-list-local.svg b/docs/images/nf-core-modules-list-local.svg
index 5d592084ac..a1b2806467 100644
--- a/docs/images/nf-core-modules-list-local.svg
+++ b/docs/images/nf-core-modules-list-local.svg
@@ -19,108 +19,108 @@
font-weight: 700;
}
- .terminal-3570470079-matrix {
+ .terminal-1750863134-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-3570470079-title {
+ .terminal-1750863134-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-3570470079-r1 { fill: #c5c8c6 }
-.terminal-3570470079-r2 { fill: #98a84b }
-.terminal-3570470079-r3 { fill: #9a9b99 }
-.terminal-3570470079-r4 { fill: #608ab1 }
-.terminal-3570470079-r5 { fill: #d0b344 }
-.terminal-3570470079-r6 { fill: #c5c8c6;font-weight: bold }
-.terminal-3570470079-r7 { fill: #868887;font-style: italic; }
+ .terminal-1750863134-r1 { fill: #c5c8c6 }
+.terminal-1750863134-r2 { fill: #98a84b }
+.terminal-1750863134-r3 { fill: #9a9b99 }
+.terminal-1750863134-r4 { fill: #608ab1 }
+.terminal-1750863134-r5 { fill: #d0b344 }
+.terminal-1750863134-r6 { fill: #c5c8c6;font-weight: bold }
+.terminal-1750863134-r7 { fill: #868887;font-style: italic; }
-
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@@ -132,36 +132,36 @@
-
+
-
- $ nf-core modules list local
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
- nf-core/tools version 2.11 - https://nf-co.re
-
-
-
-INFO Modules installed in '.':
-
-┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓
-┃Module Name ┃Repository ┃Version SHA ┃Message ┃Date ┃
-┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩
-│ custom/dumpsoftwar… │ https://github.co… │ bba7e362e4afead706… │ add │ 2023-11-14 │
-│ │ │ │ environment-schem… │ │
-│ │ │ │ rename yaml-schema │ │
-│ │ │ │ to meta-schema │ │
-│ │ │ │ (#4323) │ │
-│ fastqc │ https://github.co… │ 65ad3e0b9a4099592e… │ Update version │ 2023-12-08 │
-│ │ │ │ strings (#4556) │ │
-│ multiqc │ https://github.co… │ 4ab13872435962dadc… │ Pull multiqc │ 2023-12-05 │
-│ │ │ │ static multiqc │ │
-[..truncated..]
+
+ $ nf-core modules list local
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ nf-core/tools version 2.11.1 - https://nf-co.re
+
+
+
+INFO Modules installed in '.':
+
+┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓
+┃Module Name ┃Repository ┃Version SHA ┃Message ┃Date ┃
+┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩
+│ custom/dumpsoftwar… │ https://github.co… │ bba7e362e4afead706… │ add │ 2023-11-14 │
+│ │ │ │ environment-schem… │ │
+│ │ │ │ rename yaml-schema │ │
+│ │ │ │ to meta-schema │ │
+│ │ │ │ (#4323) │ │
+│ fastqc │ https://github.co… │ 65ad3e0b9a4099592e… │ Update version │ 2023-12-08 │
+│ │ │ │ strings (#4556) │ │
+│ multiqc │ https://github.co… │ 4ab13872435962dadc… │ Pull multiqc │ 2023-12-05 │
+│ │ │ │ static multiqc │ │
+[..truncated..]
diff --git a/docs/images/nf-core-modules-list-remote.svg b/docs/images/nf-core-modules-list-remote.svg
index 1bc0eb0ff1..28be0b24ee 100644
--- a/docs/images/nf-core-modules-list-remote.svg
+++ b/docs/images/nf-core-modules-list-remote.svg
@@ -19,109 +19,109 @@
font-weight: 700;
}
- .terminal-2130205015-matrix {
+ .terminal-2091866550-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-2130205015-title {
+ .terminal-2091866550-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-2130205015-r1 { fill: #c5c8c6 }
-.terminal-2130205015-r2 { fill: #98a84b }
-.terminal-2130205015-r3 { fill: #9a9b99 }
-.terminal-2130205015-r4 { fill: #608ab1 }
-.terminal-2130205015-r5 { fill: #d0b344 }
-.terminal-2130205015-r6 { fill: #1984e9;text-decoration: underline; }
-.terminal-2130205015-r7 { fill: #c5c8c6;font-weight: bold }
-.terminal-2130205015-r8 { fill: #868887;font-style: italic; }
+ .terminal-2091866550-r1 { fill: #c5c8c6 }
+.terminal-2091866550-r2 { fill: #98a84b }
+.terminal-2091866550-r3 { fill: #9a9b99 }
+.terminal-2091866550-r4 { fill: #608ab1 }
+.terminal-2091866550-r5 { fill: #d0b344 }
+.terminal-2091866550-r6 { fill: #1984e9;text-decoration: underline; }
+.terminal-2091866550-r7 { fill: #c5c8c6;font-weight: bold }
+.terminal-2091866550-r8 { fill: #868887;font-style: italic; }
-
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@@ -133,36 +133,36 @@
-
+
-
- $ nf-core modules list remote
-
- ,--./,-.
- ___ __ __ __ ___ /,-._.--~\
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
- `._,._,'
-
- nf-core/tools version 2.11 - https://nf-co.re
-
-
-
-INFO Modules available from https://github.com/nf-core/modules.git(master):
-
-┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
-┃Module Name ┃
-┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
-│ abacas │
-│ abricate/run │
-│ abricate/summary │
-│ abritamr/run │
-│ adapterremoval │
-│ adapterremovalfixprefix │
-│ admixture │
-│ affy/justrma │
-│ agat/convertspgff2gtf │
-[..truncated..]
+
+ $ nf-core modules list remote
+
+ ,--./,-.
+ ___ __ __ __ ___ /,-._.--~\
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+ `._,._,'
+
+ nf-core/tools version 2.11.1 - https://nf-co.re
+
+
+
+INFO Modules available from https://github.com/nf-core/modules.git(master):
+
+┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
+┃Module Name ┃
+┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
+│ abacas │
+│ abricate/run │
+│ abricate/summary │
+│ abritamr/run │
+│ adapterremoval │
+│ adapterremovalfixprefix │
+│ admixture │
+│ affy/justrma │
+│ agat/convertspgff2gtf │
+[..truncated..]
diff --git a/docs/images/nf-core-modules-patch.svg b/docs/images/nf-core-modules-patch.svg
index 7c6973da2c..25033c107a 100644
--- a/docs/images/nf-core-modules-patch.svg
+++ b/docs/images/nf-core-modules-patch.svg
@@ -1,4 +1,4 @@
-