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Report warning message when analyzing data with two replicates #7289

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Report warning message when analyzing data with two replicates #7289

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Xinlei-Gao
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The update version deals with two cases:

  1. If there are two conditions with two replicates, skip running anota2seq and report warning message in the log file.

  2. If there are more than two conditions with two replicates, perform analysis with the parameter onlyGroup = TRUE, and report warning message in the log file.

PR checklist

Closes #XXX

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
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  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@Xinlei-Gao
Report warning message when performing translational efficiency analy…
b49fd95 
…sis on datasets with only two replicates.

The update version deals with two cases:
1. If there are two conditions with two replicates, skip running anota2seq and report warning message in the log file.

2. If there are more than two conditions with two replicates, perform analysis with the parameter onlyGroup = TRUE, and report warning message in the log file.
@lpantano
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Hi @Xinlei-Gao, did you get to run nf-core modules test <MODULE> --profile docker successfully locally? I think you need to update your snapshots and that is done by running twice the modules test (I believe).

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Xinlei-Gao commented Jan 10, 2025 via email

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Xinlei-Gao commented Jan 10, 2025 via email

@SPPearce
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I'm confused by this module, what exactly is it doing?

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Xinlei-Gao commented Jan 13, 2025 via email

SPPearce
SPPearce reviewed Jan 13, 2025
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Ok, I think I understand what the module is doing now (not the PR, the module itself), I was confused by the fact that a samplesheet was being passed.

modules/nf-core/anota2seq/anota2seqrun/main.nf
@@ -33,5 +33,7 @@ process ANOTA2SEQ_ANOTA2SEQRUN {
task.ext.when == null || task.ext.when

script:
template 'anota2seqrun.r'
"""
Rscript ${projectDir}/modules/nf-core/anota2seq/anota2seqrun/templates/anota2seqrun.r --output_prefix ${task.ext.prefix ?: meta.id} --sample_treatment_col ${sample_treatment_col} --reference_level ${reference} --target_level ${target} --sample_file ${samplesheet} --count_file ${counts}
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You can't do this, it won't work on cloud providers. Why are you trying to move away from the use of the template?

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Xinlei-Gao commented Jan 13, 2025 via email

@SPPearce
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I tried keeping using template after modifying the R code anota2seqrun.r, but it failed when I ran the nf-core Ribo-seq pipeline (which called this module), due to some error that it can not correctly pass the parameter like $task.ext.***. So that I replaced the template command with directly calling Rscript and passing the parameters in the command line. The template R script itself would read an input samplesheet. The samplesheet file is provided in a nf-core test dataset. I don't know this can affect cloud platforms. If so what might be any suggestions? Thanks! Xinlei

Guidelines are here: https://nf-co.re/docs/guidelines/components/modules#script-inclusion
I think we should be able to fix the template issue, we should be able to use task.ext.args with the template.

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@Xinlei-Gao @lpantano @SPPearce