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Added light mode plots #27

Merged
merged 9 commits into from
May 15, 2024
Merged

Added light mode plots #27

merged 9 commits into from
May 15, 2024

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itrujnara
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Closes #14

  • Added light mode plots
  • Changed modules and subworkflows accordingly

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint). Something something template, passes on GitHub.
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).

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github-actions bot commented May 14, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5a60c26

+| ✅ 216 tests passed       |+
!| ❗  13 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • 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 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 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 ci.yml: You can customise CI pipeline run tests as required
  • 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 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-15 08:43:50

JoseEspinosa
JoseEspinosa requested changes May 14, 2024
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Some suggestions and questions 😄

bin/plot_orthologs.R Outdated Show resolved Hide resolved
modules/local/plot_tree.nf Outdated Show resolved Hide resolved
modules/local/plot_orthologs.nf Outdated Show resolved Hide resolved
subworkflows/local/get_orthologs.nf Outdated Show resolved Hide resolved
subworkflows/local/make_trees.nf Outdated Show resolved Hide resolved
subworkflows/local/make_trees.nf Outdated Show resolved Hide resolved
workflows/reportho.nf
@@ -94,8 +94,8 @@ workflow REPORTHO {
ALIGN.out.alignment
)

ch_iqtree = MAKE_TREES.out.mlplot
ch_fastme = MAKE_TREES.out.meplot
ch_iqtree = MAKE_TREES.out.mlplot.map { [it[0], it[1]] }
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Maybe I am not understanding, but here you want to pass both the dark and light plots, right? if yes, won't be it[1] and it[2]?

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This is the part related to the report, so only the dark mode plots are necessary, as the report is in dark mode. The meta is passed because the subworkflow uses it to organize the files.

itrujnara and others added 7 commits May 15, 2024 10:35
@itrujnara @JoseEspinosa
Update bin/plot_orthologs.R
20aee56 
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
@itrujnara @JoseEspinosa
Update modules/local/plot_orthologs.nf
184893a 
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
@itrujnara @JoseEspinosa
Update modules/local/plot_tree.nf
ad2d0dc 
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
@itrujnara @JoseEspinosa
Update subworkflows/local/get_orthologs.nf
c0ea378 
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
@itrujnara @JoseEspinosa
Update subworkflows/local/make_trees.nf
e4db509 
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
@itrujnara @JoseEspinosa
Update subworkflows/local/make_trees.nf
36553b8 
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
@itrujnara
Make prettier happy
5a60c26
JoseEspinosa
JoseEspinosa approved these changes May 15, 2024
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LGTM! 🚀

@JoseEspinosa JoseEspinosa merged commit a1d3af7 into nf-core:dev May 15, 2024
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@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

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Add light mode plots
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@itrujnara @JoseEspinosa