64 lines
1.7 KiB
Plaintext
64 lines
1.7 KiB
Plaintext
nextflow.enable.dsl = 2
|
|
|
|
|
|
process checkExperimentDesign {
|
|
label "wf_common"
|
|
cpus 1
|
|
memory "2 GB"
|
|
input:
|
|
path sample_sheet
|
|
output:
|
|
path "validated.ok", emit: ok
|
|
script:
|
|
String covariates_arg = params.covariates ? "--covariates '${params.covariates}'" : ""
|
|
String reference_arg = params.reference_level ? "--reference_level '${params.reference_level}'" : ""
|
|
"""
|
|
workflow-glue check_experiment_design \
|
|
--sample_sheet "${sample_sheet}" \
|
|
--condition_column "${params.condition_column}" \
|
|
${covariates_arg} \
|
|
${reference_arg}
|
|
touch validated.ok
|
|
"""
|
|
}
|
|
|
|
|
|
process runDifferentialAnalysis {
|
|
label "wf_transcriptomes"
|
|
cpus { params.threads ?: 4 }
|
|
memory "32 GB"
|
|
input:
|
|
path transcript_rds
|
|
path gene_rds
|
|
path sample_sheet
|
|
path validation_token
|
|
output:
|
|
path "de_analysis", emit: dir
|
|
script:
|
|
String covariates_arg = params.covariates ? "--covariates '${params.covariates}'" : ""
|
|
String reference_arg = params.reference_level ? "--reference_level '${params.reference_level}'" : ""
|
|
"""
|
|
supeRglue de_analysis \
|
|
--transcript_rds "${transcript_rds}" \
|
|
--gene_rds "${gene_rds}" \
|
|
--sample_sheet "${sample_sheet}" \
|
|
--condition_column "${params.condition_column}" \
|
|
${covariates_arg} \
|
|
${reference_arg} \
|
|
--out_dir de_analysis
|
|
"""
|
|
}
|
|
|
|
|
|
workflow differential_expression {
|
|
take:
|
|
transcript_rds
|
|
gene_rds
|
|
sample_sheet
|
|
main:
|
|
validated = checkExperimentDesign(sample_sheet)
|
|
results = runDifferentialAnalysis(transcript_rds, gene_rds, sample_sheet, validated.ok)
|
|
emit:
|
|
dir = results.dir
|
|
}
|