Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

nf-test: utils_nfcore_rnaseq_pipeline tests #1235

Merged
merged 8 commits into from
Mar 6, 2024
Merged

nf-test: utils_nfcore_rnaseq_pipeline tests #1235

Show file tree
Hide file tree
Changes from 4 commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions main.nf
View file
Open in desktop
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,
Expand Down
13 changes: 8 additions & 5 deletions subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
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 Expand Up @@ -507,6 +509,7 @@ def getStarPercentMapped(params, align_log) {
align_log.eachLine { line ->
def matcher = line =~ pattern
if (matcher) {
println matcher[0][1].toFloat()
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Assume this is going?

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Blast!

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Fixed now.

adamrtalbot marked this conversation as resolved.
Show resolved Hide resolved
percent_aligned = matcher[0][1].toFloat()
}
}
Expand Down
Loading
Loading