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extract -> get
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@maxulysse
maxulysse committed Feb 3, 2025
1 parent 28440fa commit 88755d5
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Showing 2 changed files with 41 additions and 41 deletions.
74 changes: 37 additions & 37 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -32,8 +32,8 @@ include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfc
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_sarek_pipeline'
include { PREPARE_INTERVALS } from './subworkflows/local/prepare_intervals'
include { PREPARE_REFERENCE_CNVKIT } from './subworkflows/local/prepare_reference_cnvkit'
include { extract_references_file } from './subworkflows/local/utils_references'
include { extract_references_value } from './subworkflows/local/utils_references'
include { get_references_file } from './subworkflows/local/utils_references'
include { get_references_value } from './subworkflows/local/utils_references'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -85,45 +85,45 @@ workflow NFCORE_SAREK {
versions = Channel.empty()

// References' files from the references yaml or params
ascat_alleles = extract_references_file(references, params.ascat_alleles, 'ascat_alleles', params.igenomes_base)
ascat_loci = extract_references_file(references, params.ascat_loci, 'ascat_loci', params.igenomes_base)
ascat_loci_gc = extract_references_file(references, params.ascat_loci_gc, 'ascat_loci_gc', params.igenomes_base)
ascat_loci_rt = extract_references_file(references, params.ascat_loci_rt, 'ascat_loci_rt', params.igenomes_base)
bwamem1_index = extract_references_file(references, params.bwa, 'bwamem1_index', params.igenomes_base)
bwamem2_index = extract_references_file(references, params.bwamem2, 'bwamem2_index', params.igenomes_base)
cf_chrom_len = extract_references_file(references, params.cf_chrom_len, 'cf_chrom_len', params.igenomes_base)
chr_dir = extract_references_file(references, params.chr_dir, 'chr_dir', params.igenomes_base)
dragmap_hashtable = extract_references_file(references, params.dragmap, 'dragmap_hashtable', params.igenomes_base)
fasta = extract_references_file(references, params.fasta, 'fasta', params.igenomes_base)
fasta_dict = extract_references_file(references, params.dict, 'fasta_dict', params.igenomes_base)
fasta_fai = extract_references_file(references, params.fasta_fai, 'fasta_fai', params.igenomes_base)
intervals_bed = extract_references_file(references, params.intervals, 'intervals_bed', params.igenomes_base)
mappability = extract_references_file(references, params.mappability, 'mappability', params.igenomes_base)
msisensorpro_scan = extract_references_file(references, params.msisensorpro_scan, 'msisensorpro_scan', params.igenomes_base)
ngscheckmate_bed = extract_references_file(references, params.ngscheckmate_bed, 'ngscheckmate_bed', params.igenomes_base)
sentieon_dnascope_model = extract_references_file(references, params.sentieon_dnascope_model, 'sentieon_dnascope_model', params.igenomes_base)
ascat_alleles = get_references_file(references, params.ascat_alleles, 'ascat_alleles', params.igenomes_base)
ascat_loci = get_references_file(references, params.ascat_loci, 'ascat_loci', params.igenomes_base)
ascat_loci_gc = get_references_file(references, params.ascat_loci_gc, 'ascat_loci_gc', params.igenomes_base)
ascat_loci_rt = get_references_file(references, params.ascat_loci_rt, 'ascat_loci_rt', params.igenomes_base)
bwamem1_index = get_references_file(references, params.bwa, 'bwamem1_index', params.igenomes_base)
bwamem2_index = get_references_file(references, params.bwamem2, 'bwamem2_index', params.igenomes_base)
cf_chrom_len = get_references_file(references, params.cf_chrom_len, 'cf_chrom_len', params.igenomes_base)
chr_dir = get_references_file(references, params.chr_dir, 'chr_dir', params.igenomes_base)
dragmap_hashtable = get_references_file(references, params.dragmap, 'dragmap_hashtable', params.igenomes_base)
fasta = get_references_file(references, params.fasta, 'fasta', params.igenomes_base)
fasta_dict = get_references_file(references, params.dict, 'fasta_dict', params.igenomes_base)
fasta_fai = get_references_file(references, params.fasta_fai, 'fasta_fai', params.igenomes_base)
intervals_bed = get_references_file(references, params.intervals, 'intervals_bed', params.igenomes_base)
mappability = get_references_file(references, params.mappability, 'mappability', params.igenomes_base)
msisensorpro_scan = get_references_file(references, params.msisensorpro_scan, 'msisensorpro_scan', params.igenomes_base)
ngscheckmate_bed = get_references_file(references, params.ngscheckmate_bed, 'ngscheckmate_bed', params.igenomes_base)
sentieon_dnascope_model = get_references_file(references, params.sentieon_dnascope_model, 'sentieon_dnascope_model', params.igenomes_base)

// References' values from the references yaml or params
ascat_genome = extract_references_value(references, params.ascat_genome, 'ascat_genome')
snpeff_db = extract_references_value(references, params.snpeff_db, 'snpeff_db')
vep_cache_version = extract_references_value(references, params.vep_cache_version, 'vep_cache_version')
vep_genome = extract_references_value(references, params.vep_genome, 'vep_genome')
vep_species = extract_references_value(references, params.vep_species, 'vep_species')
ascat_genome = get_references_value(references, params.ascat_genome, 'ascat_genome')
snpeff_db = get_references_value(references, params.snpeff_db, 'snpeff_db')
vep_cache_version = get_references_value(references, params.vep_cache_version, 'vep_cache_version')
vep_genome = get_references_value(references, params.vep_genome, 'vep_genome')
vep_species = get_references_value(references, params.vep_species, 'vep_species')

// References' VCFs and related from the references yaml or params
dbsnp = extract_references_file(references, params.dbsnp, 'vcf_dbsnp_vcf', params.igenomes_base)
dbsnp_tbi = extract_references_file(references, params.dbsnp_tbi, 'vcf_dbsnp_vcf_tbi', params.igenomes_base)
dbsnp_vqsr = extract_references_value(references, params.dbsnp_vqsr, 'vcf_dbsnp_vcf_vqsr')
germline_resource = extract_references_file(references, params.germline_resource, 'vcf_germline_resource_vcf', params.igenomes_base)
germline_resource_tbi = extract_references_file(references, params.germline_resource_tbi, 'vcf_germline_resource_vcf_tbi', params.igenomes_base)
known_indels = extract_references_file(references, params.known_indels, 'vcf_known_indels_vcf', params.igenomes_base)
known_indels_tbi = extract_references_file(references, params.known_indels_tbi, 'vcf_known_indels_vcf_tbi', params.igenomes_base)
known_indels_vqsr = extract_references_value(references, params.known_indels_vqsr, 'vcf_known_indels_vcf_vqsr')
known_snps = extract_references_file(references, params.known_snps, 'vcf_known_snps_vcf', params.igenomes_base)
known_snps_tbi = extract_references_file(references, params.known_snps_tbi, 'vcf_known_snps_vcf_tbi', params.igenomes_base)
known_snps_vqsr = extract_references_value(references, params.known_snps_vqsr, 'vcf_known_snps_vcf_vqsr')
pon = extract_references_file(references, params.pon, 'vcf_pon_vcf', params.igenomes_base)
pon_tbi = extract_references_file(references, params.pon_tbi, 'vcf_pon_vcf_tbi', params.igenomes_base)
dbsnp = get_references_file(references, params.dbsnp, 'vcf_dbsnp_vcf', params.igenomes_base)
dbsnp_tbi = get_references_file(references, params.dbsnp_tbi, 'vcf_dbsnp_vcf_tbi', params.igenomes_base)
dbsnp_vqsr = get_references_value(references, params.dbsnp_vqsr, 'vcf_dbsnp_vcf_vqsr')
germline_resource = get_references_file(references, params.germline_resource, 'vcf_germline_resource_vcf', params.igenomes_base)
germline_resource_tbi = get_references_file(references, params.germline_resource_tbi, 'vcf_germline_resource_vcf_tbi', params.igenomes_base)
known_indels = get_references_file(references, params.known_indels, 'vcf_known_indels_vcf', params.igenomes_base)
known_indels_tbi = get_references_file(references, params.known_indels_tbi, 'vcf_known_indels_vcf_tbi', params.igenomes_base)
known_indels_vqsr = get_references_value(references, params.known_indels_vqsr, 'vcf_known_indels_vcf_vqsr')
known_snps = get_references_file(references, params.known_snps, 'vcf_known_snps_vcf', params.igenomes_base)
known_snps_tbi = get_references_file(references, params.known_snps_tbi, 'vcf_known_snps_vcf_tbi', params.igenomes_base)
known_snps_vqsr = get_references_value(references, params.known_snps_vqsr, 'vcf_known_snps_vcf_vqsr')
pon = get_references_file(references, params.pon, 'vcf_pon_vcf', params.igenomes_base)
pon_tbi = get_references_file(references, params.pon_tbi, 'vcf_pon_vcf_tbi', params.igenomes_base)

// known_sites is made by grouping both the dbsnp and the known snps/indels resources
// Which can either or both be optional
Expand Down
8 changes: 4 additions & 4 deletions subworkflows/local/utils_references/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,8 @@ workflow UTILS_REFERENCES {

main:
// GIVING up writing a test for the functions, so writing a subworkflow to test it
references_file = extract_references_file(references, param_file, attribute_file, basepath)
references_value = extract_references_value(references, param_value, attribute_value)
references_file = get_references_file(references, param_file, attribute_file, basepath)
references_value = get_references_value(references, param_value, attribute_value)

emit:
references_file
Expand All @@ -25,7 +25,7 @@ workflow UTILS_REFERENCES {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

def extract_references_file(references, param, attribute, basepath) {
def get_references_file(references, param, attribute, basepath) {
return references
.map { meta, _readme ->
if (param || meta[attribute]) {
Expand All @@ -38,7 +38,7 @@ def extract_references_file(references, param, attribute, basepath) {
.collect()
}

def extract_references_value(references, param, attribute) {
def get_references_value(references, param, attribute) {
return references
.map { meta, _readme ->
if (param || meta[attribute]) {
Expand Down

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