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nf-test: utils_nfcore_rnaseq_pipeline tests #1235

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merged 8 commits into from
Mar 6, 2024
Merged

nf-test: utils_nfcore_rnaseq_pipeline tests #1235

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18fcdbd
Add nf-tests for nf-core/rnaseq utility functions
adamrtalbot Mar 6, 2024
c988ce0
Adds tests for nf-core/rnaseq utility subworkflows
adamrtalbot Mar 6, 2024
fce6bfb
Merge branch 'dev' into nf-test-utils_nfcore_rnaseq_pipeline
adamrtalbot Mar 6, 2024
fbb6992
Fix using schema variable correctly in PIPELINE_COMPLETION
adamrtalbot Mar 6, 2024
6bf28ae
test tidy
adamrtalbot Mar 6, 2024
2f90516
Update subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
adamrtalbot Mar 6, 2024
5ef27d8
Merge branch 'dev' into nf-test-utils_nfcore_rnaseq_pipeline
adamrtalbot Mar 6, 2024
f8f493c
fix snap
adamrtalbot Mar 6, 2024
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2 changes: 2 additions & 0 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -145,6 +145,7 @@ workflow {
PIPELINE_INITIALISATION (
params.version,
params.help,
"nextflow_schema.json",
params.validate_params,
params.monochrome_logs,
args,
Expand All @@ -160,6 +161,7 @@ workflow {
// SUBWORKFLOW: Run completion tasks
//
PIPELINE_COMPLETION (
"nextflow_schema.json",
params.email,
params.email_on_fail,
params.plaintext_email,
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12 changes: 7 additions & 5 deletions subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
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Expand Up @@ -32,9 +32,10 @@ workflow PIPELINE_INITIALISATION {
take:
version // boolean: Display version and exit
help // boolean: Display help text
schema // string: Path to the JSON schema file
validate_params // boolean: Boolean whether to validate parameters against the schema at runtime
monochrome_logs // boolean: Do not use coloured log outputs
nextflow_cli_args // array: List of positional nextflow CLI args
nextflow_cli_args // array: List of positional nextflow CLI args
outdir // string: The output directory where the results will be saved

main:
Expand All @@ -61,7 +62,7 @@ workflow PIPELINE_INITIALISATION {
pre_help_text,
post_help_text,
validate_params,
"nextflow_schema.json"
schema
)

//
Expand All @@ -87,6 +88,7 @@ workflow PIPELINE_INITIALISATION {
workflow PIPELINE_COMPLETION {

take:
schema // string: Path to the JSON schema file
email // string: email address
email_on_fail // string: email address sent on pipeline failure
plaintext_email // boolean: Send plain-text email instead of HTML
Expand All @@ -97,7 +99,7 @@ workflow PIPELINE_COMPLETION {

main:

summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
summary_params = paramsSummaryMap(workflow, parameters_schema: schema)

//
// Completion email and summary
Expand All @@ -122,9 +124,9 @@ workflow PIPELINE_COMPLETION {
*/

//
// Function to validate channels from input samplesheet
// Function to check samples are internally consistent after being grouped
//
def validateInputSamplesheet(input) {
def checkSamplesAreConsistent(input) {
def (metas, fastqs) = input[1..2]

// Check that multiple runs of the same sample are of the same strandedness
Expand Down
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