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Documentation update and added a full test #67

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Documentation update and added a full test #67

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RobJY
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@RobJY RobJY commented Oct 31, 2024

I've made another pass or two through the documentation. It still needs work, but I'm starting a pull request so we can discuss.

This also adds a full test that can be run with:
nextflow run . -profile test_full,docker --outdir <OUTDIR>

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/mcmicro branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@RobJY
added more to README; pushing to GitHub to see how it looks there
be1ea6b
@RobJY
fixed README bugs
d3f85c7
@RobJY
more fixes to README
a6d5343
@RobJY
another README fix
d74397e
@RobJY
updated usage doc
1c1a927
@RobJY
just a checkpoint
c4cf4ed
@RobJY
Merge branch 'dev' into documentation
bc1af39
@RobJY
just saving current state of output.md
47f176d
@RobJY
added more to usage doc
d552812
@RobJY
small change to usage doc
8960f1d
@RobJY
updated and cleaned-up output doc
c82929e
@RobJY
output doc fixes
3f205bd
@RobJY
lint fixes
c82de83
@RobJY
fixed subworkflow publication lint warnings
ae3eb7b
@RobJY
had already fixed last pub related lint message
84b0f36
@RobJY
added full_test
15add0e
@RobJY
updated ci for testing
d262c32
@RobJY
ci testing
d3b9b4b
@RobJY
ci testing
142bfa1
@RobJY
ci testing
3903510
@RobJY
ci testing
fec00ed
@RobJY
ci testing
5fc0b8e
@RobJY
ci testing
b808668
@RobJY
ci testing
54a4020
@RobJY
ci testing
5c52969
@RobJY
ci tests
18c1d9b
@RobJY
ci testing
88e48b7
@RobJY
ci testing
3f78d5b
@RobJY
ci testing
b2a0c38
@RobJY
ci testing
aea8a73
@RobJY RobJY requested a review from jmuhlich October 31, 2024 18:03
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github-actions bot commented Oct 31, 2024 •
edited
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 31a28e7

+| ✅ 167 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  14 tests had warnings |!
-| ❌  13 tests failed       |-

❌ Test failures:

  • nextflow_config - Config variable (incorrectly) found: params.max_cpus
  • nextflow_config - Config variable (incorrectly) found: params.max_memory
  • nextflow_config - Config variable (incorrectly) found: params.max_time
  • nextflow_config - Old lines for loading custom profiles found. File should contain: ```groovy
    // Load nf-core custom profiles from different Institutions
    includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - .gitignore does not match the template
  • actions_ci - '.github/workflows/ci.yml' is not triggered on expected events
  • actions_ci - Minimum pipeline NF version '23.04.0' is not tested in '.github/workflows/ci.yml'
  • actions_awsfulltest - .github/workflows/awsfulltest.yml is not triggered correctly
  • multiqc_config - assets/multiqc_config.yml does not contain a matching 'report_comment'.
    The expected comment is:
    This report has been generated by the <a href="https://github.com/nf-core/mcmicro/tree/dev" target="_blank">nf-core/mcmicro</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/mcmicro/dev/docs/output" target="_blank">documentation</a>.
    The current comment is:
    This report has been generated by the <a href="https://github.com/nf-core/mcmicro/releases/tag/2.0.0" target="_blank">nf-core/mcmicro</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/mcmicro/2.0.0/docs/output" target="_blank">documentation</a>.

❗ Test warnings:

  • files_exist - File not found: conf/igenomes_ignored.config
  • nextflow_config - nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in ci.yml: # You can customise CI pipeline run tests as required
  • schema_lint - Parameter input not found in schema
  • nfcore_yml - nf-core version in .nf-core.yml is not set to the latest version. Should be 3.0.2 but was 3.0.1

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-31 18:40:04

@kbestak
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kbestak commented Nov 4, 2024

As with the other PR, let's first merge the template update, then resolve conflicts as I see a lot of repeated changes between this, and #66.

@RobJY
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RobJY commented Nov 4, 2024

Sounds good. I was trying to work around things that would be effected by the template merge.

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@jmuhlich jmuhlich Awaiting requested review from jmuhlich

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