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

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Nov 20, 2024
Merged

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

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037581b
Fix params validation
JoseEspinosa Nov 20, 2024
3269793
Update changelog
JoseEspinosa Nov 20, 2024
4addb4b
Make lint happy
JoseEspinosa Nov 20, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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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 |
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34 changes: 23 additions & 11 deletions main.nf
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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)
//
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27 changes: 0 additions & 27 deletions subworkflows/local/utils_nfcore_chipseq_pipeline/main.nf
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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
//
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