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Fix typos #196

Merged
merged 12 commits into from
Sep 17, 2024
Merged

Fix typos #196

merged 12 commits into from
Sep 17, 2024

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LaurenceKuhl
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Hey I had a few typos laying around and forgot to include the version on some modules :)

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github-actions bot commented Sep 16, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f8e11ea

+| ✅ 229 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • 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!

❔ Tests ignored:

  • files_exist - File is ignored: conf/test.config
  • files_exist - File is ignored: conf/test_full.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-17 07:33:35

mirpedrol
mirpedrol approved these changes Sep 16, 2024
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docs/usage/screening.md Outdated Show resolved Hide resolved
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modules/local/venndiagram.nf Outdated
Comment on lines 53 to 54
ggsave(paste0("venn_",name,"_mageckmle.png"),plot_test)
write.table(common_genes, paste0('${prefix}_',name_module,"_common_genes_mle.txt"),sep = "\t", quote = FALSE, row.names=FALSE)
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name seems to be sample dependent, and name_module the name of the tool. Just wanted to make sure that using different names to save the plot and the table is intended, should we maybe use both?

workflows/crisprseq_screening.nf Outdated
}

if(params.mle && params.drugz) {
ch_venndiagram = DRUGZ.out.per_gene_results.join(MAGECK_MLE.out.gene_summary)
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can bagel2 and drugz both run in the same analysis? We should give the channel a different name to avoid overriding problems.

@LaurenceKuhl LaurenceKuhl merged commit 72134bb into nf-core:dev Sep 17, 2024
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@LaurenceKuhl LaurenceKuhl deleted the params branch September 17, 2024 08:05
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@mirpedrol mirpedrol mirpedrol approved these changes

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@LaurenceKuhl @mirpedrol