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fix admonitions in usage.md#1853

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mashehu merged 6 commits into
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admonitions
May 11, 2026
Merged

fix admonitions in usage.md#1853
mashehu merged 6 commits into
devfrom
admonitions

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@mashehu mashehu commented May 11, 2026

Replace pre-admonition quoteblocks with nf-core flavored admonitions something similar should probably done in the readme.md and output.md

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fix admonitions in usage.md
fea953c 
Replace pre-admonition quoteblocks with nf-core [flavored admonitions](https://nf-co.re/docs/developing/documentation/website-markdown#admonitions) something similar should probably done in the readme.md and output.md
mashehu
mashehu commented May 11, 2026
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d07dee7 
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
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github-actions Bot commented May 11, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9ba6904

+| ✅ 215 tests passed       |+
#| ❔  19 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   7 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: conf/containers_conda_lock_files_amd64.config
  • files_exist - File is ignored: conf/containers_conda_lock_files_arm64.config
  • files_exist - File is ignored: conf/containers_docker_amd64.config
  • files_exist - File is ignored: conf/containers_docker_arm64.config
  • files_exist - File is ignored: conf/containers_singularity_https_amd64.config
  • files_exist - File is ignored: conf/containers_singularity_https_arm64.config
  • files_exist - File is ignored: conf/containers_singularity_oras_amd64.config
  • files_exist - File is ignored: conf/containers_singularity_oras_arm64.config
  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • nf_test_content - nf_test_content
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/nf-core-rnaseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-rnaseq_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_nf_test - actions_nf_test
  • modules_config - modules_config
  • container_configs - container_configs

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-05-11 11:57:36

pinin4fjords and others added 4 commits May 11, 2026 12:45
@pinin4fjords
Merge remote-tracking branch 'origin/dev' into pr-1853-admonitions
1f398e6
@pinin4fjords @claude
docs: extend admonition cleanup to README.md and output.md [skip ci]
06be65e 
Replace the remaining pre-admonition `> **NB:**` / `> **Note**` /
`> **Warning**` quoteblocks in README.md and docs/output.md with nf-core
flavored `:::` admonitions, matching the usage.md changes already in this
PR. GitHub-style `> [!NOTE]` / `> [!WARNING]` alerts are left alone since
they already render as admonitions. Also fixes a `k-mer size off` typo
spotted alongside the conversion.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
@pinin4fjords @claude
docs(changelog): add PR #1853 entry for admonition cleanup
e8cf37c 
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
@pinin4fjords @claude
docs(usage): tag remaining shell-snippet fences as bash
9ba6904 
Extends the ```` ``` ```` → ```` ```bash ```` change applied earlier in
this PR to the four other bare code fences in `docs/usage.md` that
contain CLI args or shell commands (`--extra_star_align_args`,
`--extra_salmon_quant_args`, UMI flags, the Ensembl curl/wget snippet).
Leaves the directory-tree fence at L472 bare since it isn't shell.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
@mashehu mashehu merged commit cda7213 into dev May 11, 2026
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@mashehu @pinin4fjords
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