Template update for nf-core/tools version 2.7.1
nf-core-bot
1 year ago
parent
51bacb00e6
commit
36f3b5723b
@ -0,0 +1,27 @@
|
||||
{
|
||||
"name": "nfcore",
|
||||
"image": "nfcore/gitpod:latest",
|
||||
"remoteUser": "gitpod",
|
||||
|
||||
// Configure tool-specific properties.
|
||||
"customizations": {
|
||||
// Configure properties specific to VS Code.
|
||||
"vscode": {
|
||||
// Set *default* container specific settings.json values on container create.
|
||||
"settings": {
|
||||
"python.defaultInterpreterPath": "/opt/conda/bin/python",
|
||||
"python.linting.enabled": true,
|
||||
"python.linting.pylintEnabled": true,
|
||||
"python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
|
||||
"python.formatting.yapfPath": "/opt/conda/bin/yapf",
|
||||
"python.linting.flake8Path": "/opt/conda/bin/flake8",
|
||||
"python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
|
||||
"python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
|
||||
"python.linting.pylintPath": "/opt/conda/bin/pylint"
|
||||
},
|
||||
|
||||
// Add the IDs of extensions you want installed when the container is created.
|
||||
"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -1,3 +1,4 @@
|
||||
*.config linguist-language=nextflow
|
||||
*.nf.test linguist-language=nextflow
|
||||
modules/nf-core/** linguist-generated
|
||||
subworkflows/nf-core/** linguist-generated
|
||||
|
||||
@ -1,56 +0,0 @@
|
||||
cff-version: 1.2.0
|
||||
message: "If you use `nf-core tools` in your work, please cite the `nf-core` publication"
|
||||
authors:
|
||||
- family-names: Ewels
|
||||
given-names: Philip
|
||||
- family-names: Peltzer
|
||||
given-names: Alexander
|
||||
- family-names: Fillinger
|
||||
given-names: Sven
|
||||
- family-names: Patel
|
||||
given-names: Harshil
|
||||
- family-names: Alneberg
|
||||
given-names: Johannes
|
||||
- family-names: Wilm
|
||||
given-names: Andreas
|
||||
- family-names: Garcia
|
||||
given-names: Maxime Ulysse
|
||||
- family-names: Di Tommaso
|
||||
given-names: Paolo
|
||||
- family-names: Nahnsen
|
||||
given-names: Sven
|
||||
title: "The nf-core framework for community-curated bioinformatics pipelines."
|
||||
version: 2.4.1
|
||||
doi: 10.1038/s41587-020-0439-x
|
||||
date-released: 2022-05-16
|
||||
url: https://github.com/nf-core/tools
|
||||
prefered-citation:
|
||||
type: article
|
||||
authors:
|
||||
- family-names: Ewels
|
||||
given-names: Philip
|
||||
- family-names: Peltzer
|
||||
given-names: Alexander
|
||||
- family-names: Fillinger
|
||||
given-names: Sven
|
||||
- family-names: Patel
|
||||
given-names: Harshil
|
||||
- family-names: Alneberg
|
||||
given-names: Johannes
|
||||
- family-names: Wilm
|
||||
given-names: Andreas
|
||||
- family-names: Garcia
|
||||
given-names: Maxime Ulysse
|
||||
- family-names: Di Tommaso
|
||||
given-names: Paolo
|
||||
- family-names: Nahnsen
|
||||
given-names: Sven
|
||||
doi: 10.1038/s41587-020-0439-x
|
||||
journal: nature biotechnology
|
||||
start: 276
|
||||
end: 278
|
||||
title: "The nf-core framework for community-curated bioinformatics pipelines."
|
||||
issue: 3
|
||||
volume: 38
|
||||
year: 2020
|
||||
url: https://dx.doi.org/10.1038/s41587-020-0439-x
|
||||
@ -0,0 +1,34 @@
|
||||
{
|
||||
"attachments": [
|
||||
{
|
||||
"fallback": "Plain-text summary of the attachment.",
|
||||
"color": "<% if (success) { %>good<% } else { %>danger<%} %>",
|
||||
"author_name": "sanger-tol/readmapping v${version} - ${runName}",
|
||||
"author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
|
||||
"text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
|
||||
"fields": [
|
||||
{
|
||||
"title": "Command used to launch the workflow",
|
||||
"value": "```${commandLine}```",
|
||||
"short": false
|
||||
}
|
||||
<%
|
||||
if (!success) { %>
|
||||
,
|
||||
{
|
||||
"title": "Full error message",
|
||||
"value": "```${errorReport}```",
|
||||
"short": false
|
||||
},
|
||||
{
|
||||
"title": "Pipeline configuration",
|
||||
"value": "<% out << summary.collect{ k,v -> k == "hook_url" ? "_${k}_: (_hidden_)" : ( ( v.class.toString().contains('Path') || ( v.class.toString().contains('String') && v.contains('/') ) ) ? "_${k}_: `${v}`" : (v.class.toString().contains('DateTime') ? ("_${k}_: " + v.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM))) : "_${k}_: ${v}") ) }.join(",\n") %>",
|
||||
"short": false
|
||||
}
|
||||
<% }
|
||||
%>
|
||||
],
|
||||
"footer": "Completed at <% out << dateComplete.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM)) %> (duration: ${duration})"
|
||||
}
|
||||
]
|
||||
}
|
||||
Loading…
Reference in New Issue