40 lines
1.0 KiB
Plaintext
40 lines
1.0 KiB
Plaintext
nextflow.enable.dsl = 2
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process runDifferentialAnalysis {
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label "wf_transcriptomes"
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cpus 4
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memory "32 GB"
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input:
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path transcript_rds
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path gene_rds
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path sample_sheet
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output:
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path "de_analysis", emit: dir
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script:
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String covariates_arg = params.covariates ? "--covariates '${params.covariates}'" : ""
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String reference_arg = params.reference_level ? "--reference_level '${params.reference_level}'" : ""
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"""
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supeRglue de_analysis \
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--transcript_rds "${transcript_rds}" \
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--gene_rds "${gene_rds}" \
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--sample_sheet "${sample_sheet}" \
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--condition_column "${params.condition_column}" \
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${covariates_arg} \
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${reference_arg} \
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--out_dir de_analysis
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"""
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}
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workflow differential_expression {
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take:
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transcript_rds
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gene_rds
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sample_sheet
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main:
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results = runDifferentialAnalysis(transcript_rds, gene_rds, sample_sheet)
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emit:
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dir = results.dir
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}
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