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Several fixes #408

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merged 7 commits into from
Jul 31, 2024
Merged

Several fixes #408

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fd28fe4
Read params before including anything
JoseEspinosa Jul 24, 2024
b1f7d31
Move getGenomeAttribute function to main
JoseEspinosa Jul 24, 2024
a20c464
Also move getMacsGsize declaration
JoseEspinosa Jul 24, 2024
50caeb9
Remove includes
JoseEspinosa Jul 24, 2024
cd28cd0
Fix output of bwa index when provided as not compressed input
JoseEspinosa Jul 25, 2024
588a28a
Make lint happy
JoseEspinosa Jul 31, 2024
49c405c
Get rid of the functions in pipeline utils
JoseEspinosa Jul 31, 2024
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57 changes: 45 additions & 12 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -11,18 +11,6 @@

nextflow.enable.dsl = 2

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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'
include { getMacsGsize } from './subworkflows/local/utils_nfcore_chipseq_pipeline'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GENOME PARAMETER VALUES
Expand All @@ -40,6 +28,18 @@ 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'
// include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_chipseq_pipeline'
// include { getMacsGsize } from './subworkflows/local/utils_nfcore_chipseq_pipeline'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOWS FOR PIPELINE
Expand Down Expand Up @@ -137,6 +137,39 @@ workflow {
)
}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
FUNCTIONS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

//
// 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)
//
def getMacsGsize(params) {
def val = null
if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
if (params.genomes[ params.genome ].containsKey('macs_gsize')) {
if (params.genomes[ params.genome ][ 'macs_gsize' ].containsKey(params.read_length.toString())) {
val = params.genomes[ params.genome ][ 'macs_gsize' ][ params.read_length.toString() ]
}
}
}
return val
}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
Expand Down
2 changes: 1 addition & 1 deletion subworkflows/local/prepare_genome.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -146,7 +146,7 @@ workflow PREPARE_GENOME {
ch_bwa_index = UNTAR_BWA_INDEX ( [ [:], bwa_index ] ).untar
ch_versions = ch_versions.mix(UNTAR_BWA_INDEX.out.versions)
} else {
ch_bwa_index = file(bwa_index)
ch_bwa_index = [ [:], file(bwa_index) ]
}
} else {
ch_bwa_index = BWA_INDEX ( ch_fasta.map { [ [:], it ] } ).index
Expand Down
27 changes: 0 additions & 27 deletions subworkflows/local/utils_nfcore_chipseq_pipeline/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -149,18 +149,6 @@ def validateInputParameters() {
}
}

//
// 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 All @@ -175,21 +163,6 @@ def genomeExistsError() {
}
}

//
// Get macs genome size (macs_gsize)
//
def getMacsGsize(params) {
def val = null
if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
if (params.genomes[ params.genome ].containsKey('macs_gsize')) {
if (params.genomes[ params.genome ][ 'macs_gsize' ].containsKey(params.read_length.toString())) {
val = params.genomes[ params.genome ][ 'macs_gsize' ][ params.read_length.toString() ]
}
}
}
return val
}

//
// Generate methods description for MultiQC
//
Expand Down
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