Skip to content

Prevent pipeline fails from erroneous param validation when igenomes is used #434

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

Merged
bjlang merged 3 commits into from
Nov 20, 2024
Merged

Prevent pipeline fails from erroneous param validation when igenomes is used #434

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
037581b
Fix params validation
JoseEspinosa Nov 20, 2024
3269793
Update changelog
JoseEspinosa Nov 20, 2024
4addb4b
Make lint happy
JoseEspinosa Nov 20, 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 CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Enhancements & fixes

[[PR #434](https://github.com/nf-core/chipseq/pull/434)] - Prevent pipeline fails from erroneous param validation when igenomes is used.

### Parameters

| Old parameter | New parameter |
Expand Down
34 changes: 23 additions & 11 deletions main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,17 +9,6 @@
----------------------------------------------------------------------------------------
*/

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { CHIPSEQ } from './workflows/chipseq'
include { PREPARE_GENOME } from './subworkflows/local/prepare_genome'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_chipseq_pipeline'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_chipseq_pipeline'
include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_chipseq_pipeline'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GENOME PARAMETER VALUES
Expand All @@ -37,6 +26,17 @@ params.gene_bed = getGenomeAttribute('gene_bed')
params.blacklist = getGenomeAttribute('blacklist')
params.macs_gsize = getMacsGsize(params)

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

include { CHIPSEQ } from './workflows/chipseq'
include { PREPARE_GENOME } from './subworkflows/local/prepare_genome'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_chipseq_pipeline'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_chipseq_pipeline'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOWS FOR PIPELINE
Expand Down Expand Up @@ -138,6 +138,18 @@ workflow {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

//
// Get attribute from genome config file e.g. fasta
//
def getGenomeAttribute(attribute) {
if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
if (params.genomes[params.genome].containsKey(attribute)) {
return params.genomes[params.genome][attribute]
}
}
return null
}

//
// Get macs genome size (macs_gsize)
//
Expand Down
27 changes: 0 additions & 27 deletions subworkflows/local/utils_nfcore_chipseq_pipeline/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -158,33 +158,6 @@ def validateInputParameters() {
}
}

//
// Validate channels from input samplesheet
//
def validateInputSamplesheet(input) {
def (metas, fastqs) = input[1..2]

// Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
def endedness_ok = metas.collect { meta -> meta.single_end }.unique().size == 1
if (!endedness_ok) {
error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}")
}

return [metas[0], fastqs]
}

//
// Get attribute from genome config file e.g. fasta
//
def getGenomeAttribute(attribute) {
if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
if (params.genomes[params.genome].containsKey(attribute)) {
return params.genomes[params.genome][attribute]
}
}
return null
}

//
// Exit pipeline if incorrect --genome key provided
//
Expand Down
⚡