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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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18 changes: 10 additions & 8 deletions modules/nf-core/anota2seq/anota2seqrun/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,13 +12,13 @@ process ANOTA2SEQ_ANOTA2SEQRUN {
tuple val(meta2), path(samplesheet), path(counts)

output:
tuple val(meta), path("*.translated_mRNA.anota2seq.results.tsv") , emit: translated_mrna
tuple val(meta), path("*.total_mRNA.anota2seq.results.tsv") , emit: total_mrna
tuple val(meta), path("*.translation.anota2seq.results.tsv") , emit: translation
tuple val(meta), path("*.buffering.anota2seq.results.tsv") , emit: buffering
tuple val(meta), path("*.mRNA_abundance.anota2seq.results.tsv") , emit: mrna_abundance
tuple val(meta), path("*.Anota2seqDataSet.rds") , emit: rdata
tuple val(meta), path("*.fold_change.png") , emit: fold_change_plot
tuple val(meta), path("*.translated_mRNA.anota2seq.results.tsv") , emit: translated_mrna, optional: true
tuple val(meta), path("*.total_mRNA.anota2seq.results.tsv") , emit: total_mrna, optional: true
tuple val(meta), path("*.translation.anota2seq.results.tsv") , emit: translation, optional: true
tuple val(meta), path("*.buffering.anota2seq.results.tsv") , emit: buffering, optional: true
tuple val(meta), path("*.mRNA_abundance.anota2seq.results.tsv") , emit: mrna_abundance, optional: true
tuple val(meta), path("*.Anota2seqDataSet.rds") , emit: rdata, optional: true
tuple val(meta), path("*.fold_change.png") , emit: fold_change_plot, optional: true
tuple val(meta), path("*.interaction_p_distribution.pdf") , emit: interaction_p_distribution_plot, optional: true
tuple val(meta), path("*.residual_distribution_summary.jpeg") , emit: residual_distribution_summary_plot, optional: true
tuple val(meta), path("*.residual_vs_fitted.jpeg") , emit: residual_vs_fitted_plot, optional: true
Expand All @@ -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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