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Update from the development fork #42

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wants to merge 236 commits into from
Closed

Update from the development fork #42

wants to merge 236 commits into from

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zachary-foster
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This is the first version of the pipeline that mostly works. Its not quite ready for a first release, but enough has changed that its worth updating the nf-core fork.

zachary-foster and others added 30 commits September 13, 2023 10:29
@zachary-foster
ensured all outputs are named by IDs and made output names more clear
b86dd0e
@zachary-foster
added SNP alignment to test input data for main report
4976227
@zachary-foster
fixed a few channel operations breaking the cache
9f4654d
@zachary-foster
added depth-based read subsetting to speed up variant calling
2e6c2a0
@zachary-foster
changed report from bookdown to quarto
ccb4557
@grunwald
test
3d054d4
@grunwald
minor
a6b736a
@zachary-foster
random changes testing things
c7559a0
@zachary-foster
merge
81357cd 
Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

# Conflicts:
#	assets/main_report/_quarto.yml
@grunwald
remove python
f0ba45d
@grunwald
added summary formatting
110c016
@grunwald
minor
4022a0f
@grunwald
date format changed
de7408e
@grunwald
date format
ea780ea
@grunwald
fixed table format
fb1790f
@grunwald
minor
cbf17ec
@grunwald
changed to having all libaries loaded in a chunk at top for the rest …
5db8232 
…of the document.
@grunwald
minor edits
39a1a86
@grunwald
added draft about stuff. maybe this could be moved to one palced and …
48c7a28 
…linked several times throughout
@grunwald
added stats for # samples
d705f4b
@grunwald
submitter names parsed
d88aa68
@grunwald
minor edits
7cd2d8e
@grunwald
minor edits
56163bb
@grunwald
minor edits
3275a98
@grunwald
minor changes
22e349f
@grunwald
changes to about
d666371
@grunwald
added contributor
bbedc80
@zachary-foster
added parameters to control subsampling
82e6ff0
@zachary-foster
Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance
0671b04
@grunwald
various changes including methods section and first citations
c4f54fe
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github-actions bot commented Jan 18, 2024 •
edited
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nf-core lint overall result: Failed ❌

Posted for pipeline commit d93ff95

+| ✅ 141 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  22 tests had warnings |!
-| ❌  25 tests failed       |-

❌ Test failures:

  • files_exist - File not found: docs/images/nf-core-plantpathsurveil_logo_light.png
  • files_exist - File not found: docs/images/nf-core-plantpathsurveil_logo_dark.png
  • nextflow_config - Config variable (incorrectly) found: params.enable_conda
  • files_unchanged - .gitattributes does not match the template
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml 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 - lib/NfcoreSchema.groovy does not match the template
  • files_unchanged - lib/NfcoreTemplate.groovy does not match the template
  • files_unchanged - .prettierignore does not match the template
  • template_strings - Found a Jinja template string in /home/runner/work/pathogensurveillance/pathogensurveillance/assets/main_report/index.qmd L103: {{< var version >}}
  • template_strings - Found a Jinja template string in /home/runner/work/pathogensurveillance/pathogensurveillance/assets/main_report/index.qmd L132: {{< bi clipboard-data >}}
  • template_strings - Found a Jinja template string in /home/runner/work/pathogensurveillance/pathogensurveillance/assets/main_report/index.qmd L722: {{< fa flask >}}
  • template_strings - Found a Jinja template string in /home/runner/work/pathogensurveillance/pathogensurveillance/assets/main_report/index.qmd L729: {{< bi sliders >}}
  • template_strings - Found a Jinja template string in /home/runner/work/pathogensurveillance/pathogensurveillance/assets/main_report/index.qmd L733: {{< bi gear-wide-connected >}}
  • template_strings - Found a Jinja template string in /home/runner/work/pathogensurveillance/pathogensurveillance/assets/main_report/index.qmd L752: {{< ai doi >}}
  • template_strings - Found a Jinja template string in /home/runner/work/pathogensurveillance/pathogensurveillance/assets/main_report/packages.bib L28: {{R Core Team}}
  • template_strings - Found a Jinja template string in /home/runner/work/pathogensurveillance/pathogensurveillance/assets/main_report/packages.bib L536: {{Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality}}
  • template_strings - Found a Jinja template string in /home/runner/work/pathogensurveillance/pathogensurveillance/assets/main_report_new/index.qmd L44: {{< ai doi >}}
  • template_strings - Found a Jinja template string in /home/runner/work/pathogensurveillance/pathogensurveillance/assets/main_report_new/packages.bib L28: {{R Core Team}}
  • template_strings - Found a Jinja template string in /home/runner/work/pathogensurveillance/pathogensurveillance/assets/main_report_new/packages.bib L516: {{Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality}}
  • template_strings - Found a Jinja template string in /home/runner/work/pathogensurveillance/pathogensurveillance/docs/presentations/pathogensurveillance_15min.odp L1777: w{{{ƶ�sçÎŶmÛ(B~NN�|}}
  • template_strings - Found a Jinja template string in /home/runner/work/pathogensurveillance/pathogensurveillance/docs/presentations/pathogensurveillance_5min.odp L3400: w{{{ƶ�sçÎŶmÛ(B~NN�|}}
  • template_strings - Found a Jinja template string in /home/runner/work/pathogensurveillance/pathogensurveillance/docs/presentations/pathogensurveillance_5min.pptx L2289: ê{{dQÝë2ÒvÚ!ë½éòw(ù®s½ðÂ��e%üñTÞå´ÈDî�P�DZ#&��ø¼aΫ�(<ætù¤ÎATÞl`»«´XXp�ïjÊNa¸°Ç�ݲ6ð@]}}

❗ Test warnings:

  • files_exist - File not found: lib/WorkflowPlantpathsurveil.groovy
  • pipeline_todos - TODO string in README.md: Write a 1-2 sentence summary of what data the pipeline is for and what it does
  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • pipeline_todos - TODO string in README.md: Update the example "typical command" below used to run the pipeline
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • 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 README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
  • pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
  • pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
  • pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
  • pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
  • pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in pathogensurveillance.nf: Add all file path parameters for the pipeline to the list below
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • schema_lint - Schema $id should be https://raw.githubusercontent.com/nf-core/plantpathsurveil/master/nextflow_schema.json
    Found https://raw.githubusercontent.com/nf-core/pathogensurveillance/master/nextflow_schema.json

❔ Tests ignored:

  • files_unchanged - File does not exist: docs/images/nf-core-plantpathsurveil_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-plantpathsurveil_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2024-01-23 19:39:40

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4 participants
@zachary-foster @grunwald @cahuparo @marinawitherell