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Crisprcleanr different input (csv and defined library) #109

Merged
merged 22 commits into from
Feb 15, 2024
Merged

Crisprcleanr different input (csv and defined library) #109

merged 22 commits into from
Feb 15, 2024

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LaurenceKuhl
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@LaurenceKuhl LaurenceKuhl commented Jan 29, 2024 •
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This PR contains the following :

  • fix the matrice creation so that the user can provided a contrast table which generates the design matrices for mageck mle
  • modify the crisprcleanr module so that it can take several outputs
  • modify the docs
  • Finish documentation
  • Diff the modules between the modules repo
  • Update changelog

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github-actions bot commented Jan 29, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b73a0d4

+| ✅ 181 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowCrisprseq.groovy: Optionally add in-text citation tools to this list.
  • 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 ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-15 15:17:51

@LaurenceKuhl
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I'm a bit confused why the tests are failing for targeted given that I didn't touch anything on that side?

mirpedrol
mirpedrol reviewed Feb 8, 2024
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modules/nf-core/mageck/mle/main.nf Show resolved Hide resolved
workflows/crisprseq_screening.nf Outdated Show resolved Hide resolved
docs/usage/screening.md Outdated Show resolved Hide resolved
docs/usage/screening.md Outdated Show resolved Hide resolved
@LaurenceKuhl @mirpedrol
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4fc737a 
Co-authored-by: Júlia Mir Pedrol <[email protected]>
mirpedrol
mirpedrol approved these changes Feb 14, 2024
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LGTM! Only a couple of comments left

workflows/crisprseq_screening.nf Outdated Show resolved Hide resolved
workflows/crisprseq_screening.nf Outdated
if(params.crisprcleanr.endsWith(".csv")) {
ch_crisprcleanr_file = file(params.crisprcleanr)
} else {
ch_crisprcleanr_value = Channel.value(params.crisprcleanr)
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If I understand from the code below, you can define the same channel name, for example ch_crisprcleanr, instead of having two different channels ch_crisprcleanr_file and ch_crisprcleanr_value

workflows/crisprseq_screening.nf
) } else
{
ch_crispr_normalize = Channel.of([id: "count_table_normalize"]).concat(ch_counts)
CRISPRCLEANR_NORMALIZE(
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Have you checked if you get a warning complaining about a module used twice? You may need to import the module twice, one with an alias.

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No it doesn't complain

@LaurenceKuhl LaurenceKuhl merged commit 4d1f709 into nf-core:dev Feb 15, 2024
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@LaurenceKuhl @mirpedrol