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feat: Add unique run name configuration to ensure compatibility with Tower #20

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feat: Add unique run name configuration to ensure compatibility with Tower #20

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c9a7620
Add run name to NEXTFLOW_RUN
beatrizsavinhas Sep 2, 2026
9beb312
Add val_case_id to child pipeline calls
beatrizsavinhas Sep 2, 2026
1841034
Update module test.
beatrizsavinhas Sep 3, 2026
7e588d6
Use task.workflowId for log file name
beatrizsavinhas Sep 3, 2026
4c59cf3
Apply Mahesh's fix.
beatrizsavinhas Sep 3, 2026
c023e4a
Merge branch 'workflowid-tower-fix' into add-tower-configuration
beatrizsavinhas Sep 3, 2026
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8 changes: 7 additions & 1 deletion modules/local/nextflow/run/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ process NEXTFLOW_RUN {
val samplesheet // pipeline samplesheet
val additional_config // custom configs
val cache_dir // cache directory
val run_name // run name for Tower

output:
path "results", emit: output
Expand All @@ -22,11 +23,16 @@ process NEXTFLOW_RUN {
// Set cache directory so workflow can `-resume`
def cache_path = file(cache_dir)
assert cache_path.mkdirs()
// Create timestamp for an unique run name
def timestamp = new Date().format("yyyy-MM-dd_HH-mm-ss")
// Construct nextflow command
def nxf_cmd = [
'nextflow run',
'nextflow',
'-log .nextflow.log',
'run',
pipeline_name,
nextflow_opts,
"-name ${run_name}_${timestamp}",
params_file ? "-params-file $params_file" : '',
additional_config ? "-c $additional_config" : '',
samplesheet ? "--input $samplesheet" : '',
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1 change: 1 addition & 0 deletions modules/local/nextflow/run/tests/main.nf.test
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Expand Up @@ -15,6 +15,7 @@ nextflow_process {
input[3] = ''
input[4] = ''
input[5] = workflow.workDir.resolve('nf-core/demo').toUriString()
input[6] = 'test_case_id'
"""
}
}
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2 changes: 2 additions & 0 deletions workflows/oncoflow.nf
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Expand Up @@ -57,6 +57,7 @@ workflow ONCOFLOW {
val_oncoanalyser_samplesheet,
val_oncoanalyser_config ? val_oncoanalyser_config : val_config,
workflow.workDir.resolve('nf-core/oncoanalyser').toUriString(),
val_case_id,
)

def oncorefiner_params_list = getOncorefinerParamsList(
Expand All @@ -79,6 +80,7 @@ workflow ONCOFLOW {
'',
val_oncorefiner_config ? val_oncorefiner_config : val_config,
workflow.workDir.resolve('Clinical-Genomics/oncorefiner').toUriString(),
val_case_id,
)

//
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