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Fix bug in unexpected param log with false values. #871

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Merged
ewels merged 1 commit into from
Mar 12, 2021
Merged

Fix bug in unexpected param log with false values. #871

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14 changes: 4 additions & 10 deletions nf_core/pipeline-template/{{cookiecutter.name_noslash}}/lib/NfcoreSchema.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -18,13 +18,12 @@ class NfcoreSchema {
* whether the given paremeters adhere to the specificiations
*/
/* groovylint-disable-next-line UnusedPrivateMethodParameter */
private static ArrayList validateParameters(params, jsonSchema, log) {
private static void validateParameters(params, jsonSchema, log) {
def has_error = false
//=====================================================================//
// Check for nextflow core params and unexpected params
def json = new File(jsonSchema).text
def Map schemaParams = (Map) new JsonSlurper().parseText(json).get('definitions')
def specifiedParamKeys = params.keySet()
def nf_params = [
// Options for base `nextflow` command
'bg',
Expand Down Expand Up @@ -105,7 +104,7 @@ class NfcoreSchema {
}
}

for (specifiedParam in specifiedParamKeys) {
for (specifiedParam in params.keySet()) {
// nextflow params
if (nf_params.contains(specifiedParam)) {
log.error "ERROR: You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'"
Expand Down Expand Up @@ -144,26 +143,21 @@ class NfcoreSchema {
}

// Check for unexpected parameters
// Getting this message a lot for parameters that you *do* expect?
// You can make a csv list of expected params not in the schema with 'params.schema_ignore_params'
// for example, in your institutional config
if (unexpectedParams.size() > 0) {
Map colors = log_colours(params.monochrome_logs)
println ''
def warn_msg = 'Found unexpected parameters:'
for (unexpectedParam in unexpectedParams) {
warn_msg = warn_msg + "\n* --${unexpectedParam}: ${paramsJSON[unexpectedParam].toString()}"
warn_msg = warn_msg + "\n* --${unexpectedParam}: ${params[unexpectedParam].toString()}"
}
log.warn warn_msg
log.info "- ${colors.dim}(Hide this message with 'params.schema_ignore_params')${colors.reset} -"
log.info "- ${colors.dim}Ignore this warning: params.schema_ignore_params = \"${unexpectedParams.join(',')}\" ${colors.reset}"
println ''
}

if (has_error) {
System.exit(1)
}

return unexpectedParams
}

// Loop over nested exceptions and print the causingException
Expand Down
9 changes: 3 additions & 6 deletions nf_core/pipeline-template/{{cookiecutter.name_noslash}}/main.nf
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Expand Up @@ -24,9 +24,8 @@ if (params.help) {
////////////////////////////////////////////////////
/* -- VALIDATE PARAMETERS -- */
////////////////////////////////////////////////////+
def unexpectedParams = []
if (params.validate_params) {
unexpectedParams = NfcoreSchema.validateParameters(params, json_schema, log)
NfcoreSchema.validateParameters(params, json_schema, log)
}

////////////////////////////////////////////////////
Expand Down Expand Up @@ -365,10 +364,8 @@ workflow.onComplete {
}

workflow.onError {
// Print unexpected parameters
for (p in unexpectedParams) {
log.warn "Unexpected parameter: ${p}"
}
// Print unexpected parameters - easiest is to just rerun validation
NfcoreSchema.validateParameters(params, json_schema, log)
}

def checkHostname() {
Expand Down
9 changes: 5 additions & 4 deletions nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
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Expand Up @@ -12,6 +12,7 @@ params {
// TODO nf-core: Specify your pipeline's command line flags
genome = false
input = null
input_paths = null
single_end = false
outdir = './results'
publish_dir_mode = 'copy'
Expand All @@ -34,7 +35,7 @@ params {
config_profile_contact = false
config_profile_url = false
validate_params = true
schema_ignore_params = 'genomes'
schema_ignore_params = 'genomes,input_paths'

// Defaults only, expecting to be overwritten
max_memory = 128.GB
Expand All @@ -58,13 +59,13 @@ try {
}

profiles {
conda {
conda {
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud = false
process.conda = "$projectDir/environment.yml"
process.conda = "$projectDir/environment.yml"
}
debug { process.beforeScript = 'echo $HOSTNAME' }
docker {
Expand Down Expand Up @@ -101,7 +102,7 @@ profiles {
shifter.enabled = true
charliecloud.enabled = false
}
charliecloud {
charliecloud {
singularity.enabled = false
docker.enabled = false
podman.enabled = false
Expand Down
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