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Template: Do not assume pipeline name is url #3225

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merged 4 commits into from
Oct 16, 2024
Merged

Template: Do not assume pipeline name is url #3225

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4deb397
Template: Do not assume pipeline name is url
maxulysse Oct 15, 2024
5487a62
[automated] Update CHANGELOG.md
nf-core-bot Oct 15, 2024
c5cff7a
Merge branch 'dev' into maxulysse-patch-7
maxulysse Oct 15, 2024
f566981
Merge branch 'dev' into maxulysse-patch-7
mashehu Oct 15, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@

- Keep pipeline name in version.yml file ([#3223](https://github.com/nf-core/tools/pull/3223))
- Fix Manifest DOI text ([#3224](https://github.com/nf-core/tools/pull/3224))
- Do not assume pipeline name is url ([#3225](https://github.com/nf-core/tools/pull/3225))

### Download

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6 changes: 3 additions & 3 deletions nf_core/pipeline-template/nextflow.config
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Expand Up @@ -272,7 +272,7 @@ validation {
defaultIgnoreParams = ["genomes"]
help {
enabled = true
command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
command = "nextflow run {{ name }} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
fullParameter = "help_full"
showHiddenParameter = "show_hidden"
{% if is_nfcore -%}
Expand All @@ -283,15 +283,15 @@ validation {
\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m
\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m
\033[0;32m`._,._,\'\033[0m
\033[0;35m ${manifest.name} ${manifest.version}\033[0m
\033[0;35m {{ name }} ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
https://github.com/${manifest.name}/blob/master/CITATIONS.md
https://github.com/{{ name }}/blob/master/CITATIONS.md
"""{% endif %}
}{% if is_nfcore %}
summary {
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