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Prevent pipeline fails from erroneous param validation when igenomes is used #433

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Prevent pipeline fails from erroneous param validation when igenomes is used #433

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26b29a4
Add skips
JoseEspinosa Apr 24, 2023
0c6a17b
Merge branch 'fixes' of https://github.com/JoseEspinosa/nf-core-chips…
JoseEspinosa May 12, 2023
8b4aa4f
Merge remote-tracking branch 'upstream/dev' into fixes
JoseEspinosa Sep 22, 2023
432a88a
Fix typo in schema
JoseEspinosa Sep 22, 2023
7466cb3
Update schema and remove unused code due to nf-validation adoption
JoseEspinosa Sep 22, 2023
e69cd43
Merge remote-tracking branch 'upstream/dev' into fixes
JoseEspinosa Sep 27, 2023
5293f51
Merge remote-tracking branch 'upstream/dev' into fixes
JoseEspinosa Oct 7, 2024
725c533
Remove _REP from id for posterior grouping
JoseEspinosa Oct 7, 2024
81e3011
Update changelog
JoseEspinosa Oct 7, 2024
2f484d1
Merge remote-tracking branch 'upstream/dev' into fixes
JoseEspinosa Nov 20, 2024
b8ddbc3
Fix params validation
JoseEspinosa Nov 20, 2024
17c9afc
Update changelog
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 #433](https://github.com/nf-core/chipseq/pull/415)] - Prevent pipeline fails from erroneous param validation of fasta.

### Parameters

| Old parameter | New parameter |
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33 changes: 22 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 +26,16 @@ 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 +137,18 @@ 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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1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -63,6 +63,7 @@ params {
skip_spp = false
skip_igv = false
skip_multiqc = false
skip_peak_calling = false

// Options: Config
bamtools_filter_pe_config = "$projectDir/assets/bamtools_filter_pe.json"
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10 changes: 10 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -399,6 +399,16 @@
"description": "Skip MultiQC.",
"fa_icon": "fas fa-fast-forward"
},
"skip_peak_calling": {
"type": "boolean",
"description": "Skip MACS2 peak calling.",
"fa_icon": "fas fa-fast-forward"
},
"skip_reporting": {
"type": "boolean",
"description": "Skip reporting.",
"fa_icon": "fas fa-fast-forward"
},
"skip_qc": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
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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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