Is there an updated version of the

pipelines create

template.yml file (and up to date documentation on it in general)? The one listed here seems to be outdated: https://nf-co.re/docs/nf-core-tools/pipelines/create.

what problem are you finding?

Context: I want to build a new "powered by nf-core but not really nf-core" pipeline. The TUI wizard is cool and all, but I'd like to quickly create a few variants that skip some of the different optional features to get a better idea of what they do. The tooltips/help pop-ups are a great start, but still leave me with a few questions.

Slackbot trigger words: -

/help

/

\help

-

markdownhelp

-

moreinfo

/

moredetails

-

conda channels

/

bioconda channels

-

newpipeline

-

changeemail

-

slack theme

-

gif of the week

-

BINGO!

-

There should not have been any compilation from this call.

And problems with the template example on the page I linked: everything in the "template" section seems to be ignored, there is both a skip_features and skip declaration. There are inner / outer fields for org, name, description (and inner ones are ignored). The force declaration is ignored (false is registered as "force option was set). The is_nfcore option is ignored when set in the inner template field. etc 🙂 EDIT: you can see that the template example doesn't match what's in the current test template of the git repo either: https://github.com/nf-core/tools/blob/main/tests/data/pipeline_create_template_skip.yml

the

skip

is outdated,

skip_features

should be used instead

If the

.nf-core.yml

file that's created exactly matches the format of the template, it might be easiest to just generate a new one through the TUI (skipping all options), and using that as the template in the docs?

tested, everything should go outside the

template

section, except for

skip_features

, but there seems to be a bug since the skipped features are not added to the .nf-core.yml file

! This seems to work for me, and also adds everything to `.nf-core.yml`:

org: pipelineorg
name: pipelinename
description: pipelinedescription
author: pipelineauthor
version: 1.0.0dev
force: true
outdir: .
is_nfcore: false
skip_features:
    - github
    - github_badges
    - changelog
    - license
    - ci
    - test_config
    - nf-test
    - igenomes
    - modules
    - multiqc
    - fastqc
    - nf_schema
    - nf_core_configs
    - seqera_platform
    - gpu
    - codespaces
    - vscode
    - code_linters
    - citations
    - documentation
    - rocrate
    - email
    - adaptivecard
    - slackreport

oh perfect, I will update the decumentation then

Cheers!