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params.igenomes_base as arg for function
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@maxulysse
maxulysse committed Jan 31, 2025
1 parent 154c32a commit ee48616
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Showing 3 changed files with 58 additions and 56 deletions.
54 changes: 27 additions & 27 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -85,23 +85,23 @@ 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')
ascat_loci = extract_references_file(references, params.ascat_loci, 'ascat_loci')
ascat_loci_gc = extract_references_file(references, params.ascat_loci_gc, 'ascat_loci_gc')
ascat_loci_rt = extract_references_file(references, params.ascat_loci_rt, 'ascat_loci_rt')
bwamem1_index = extract_references_file(references, params.bwa, 'bwamem1_index')
bwamem2_index = extract_references_file(references, params.bwamem2, 'bwamem2_index')
cf_chrom_len = extract_references_file(references, params.cf_chrom_len, 'cf_chrom_len')
chr_dir = extract_references_file(references, params.chr_dir, 'chr_dir')
dragmap_hashtable = extract_references_file(references, params.dragmap, 'dragmap_hashtable')
fasta = extract_references_file(references, params.fasta, 'fasta')
fasta_dict = extract_references_file(references, params.dict, 'fasta_dict')
fasta_fai = extract_references_file(references, params.fasta_fai, 'fasta_fai')
intervals_bed = extract_references_file(references, params.intervals, 'intervals_bed')
mappability = extract_references_file(references, params.mappability, 'mappability')
msisensorpro_scan = extract_references_file(references, params.msisensorpro_scan, 'msisensorpro_scan')
ngscheckmate_bed = extract_references_file(references, params.ngscheckmate_bed, 'ngscheckmate_bed')
sentieon_dnascope_model = extract_references_file(references, params.sentieon_dnascope_model, 'sentieon_dnascope_model')
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)

// References' values from the references yaml or params
ascat_genome = extract_references_value(references, params.ascat_genome, 'ascat_genome')
Expand All @@ -111,19 +111,19 @@ workflow NFCORE_SAREK {
vep_species = extract_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')
dbsnp_tbi = extract_references_file(references, params.dbsnp_tbi, 'vcf_dbsnp_vcf_tbi')
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')
germline_resource_tbi = extract_references_file(references, params.germline_resource_tbi, 'vcf_germline_resource_vcf_tbi')
known_indels = extract_references_file(references, params.known_indels, 'vcf_known_indels_vcf')
known_indels_tbi = extract_references_file(references, params.known_indels_tbi, 'vcf_known_indels_vcf_tbi')
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')
known_snps_tbi = extract_references_file(references, params.known_snps_tbi, 'vcf_known_snps_vcf_tbi')
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')
pon_tbi = extract_references_file(references, params.pon_tbi, 'vcf_pon_vcf_tbi')
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)

// known_sites is made by grouping both the dbsnp and the known snps/indels resources
// Which can either or both be optional
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36 changes: 19 additions & 17 deletions subworkflows/local/utils_references/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,26 +4,28 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

def extract_references_file(references, param, attribute) {
def item = references.map { meta, _readme ->
if (param || meta[attribute]) {
[meta.subMap(['id']), file(param ?: meta[attribute].replace('${params.igenomes_base}', params.igenomes_base))]
def extract_references_file(references, param, attribute, basepath) {
return references
.map { meta, _readme ->
if (param || meta[attribute]) {
[meta.subMap(['id']), file(param ?: meta[attribute].replace('${params.igenomes_base}', basepath))]
}
else {
null
}
}
else {
null
}
}
return item.collect()
.collect()
}

def extract_references_value(references, param, attribute) {
def item = references.map { meta, _readme ->
if (param || meta[attribute]) {
[meta.subMap(['id']), param ?: meta[attribute]]
}
else {
null
return references
.map { meta, _readme ->
if (param || meta[attribute]) {
[meta.subMap(['id']), param ?: meta[attribute]]
}
else {
null
}
}
}
return item.collect()
.collect()
}
24 changes: 12 additions & 12 deletions subworkflows/local/utils_references/schema_references.json
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Original file line number Diff line number Diff line change
Expand Up @@ -247,13 +247,13 @@
"pattern": "^\\S+\\.vcf\\.gz\\.tbi?$",
"errorMessage": "VCF tabix index, cannot contain spaces"
},
"vcf_dbsnp_vqsr": {
"meta": ["vcf_dbsnp_vqsr"],
"vcf_dbsnp_vcf_vqsr": {
"meta": ["vcf_dbsnp_vcf_vqsr"],
"type": "string",
"errorMessage": "VCF VQSR input, can contain spaces"
},
"vcf_dbsnp_source": {
"meta": ["vcf_dbsnp_source"],
"vcf_dbsnp_vcf_source": {
"meta": ["vcf_dbsnp_vcf_source"],
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "Source of dbsnp, cannot contain spaces"
Expand All @@ -270,8 +270,8 @@
"pattern": "^\\S+\\.vcf\\.gz\\.tbi?$",
"errorMessage": "VCF tabix index, cannot contain spaces"
},
"vcf_germline_resource_source": {
"meta": ["vcf_germline_resource_source"],
"vcf_germline_resource_vcf_source": {
"meta": ["vcf_germline_resource_vcf_source"],
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "Source of germline_resource, cannot contain spaces"
Expand All @@ -288,8 +288,8 @@
"pattern": "^\\S+\\.vcf\\.gz\\.tbi?$",
"errorMessage": "VCF tabix index, cannot contain spaces"
},
"vcf_known_indels_source": {
"meta": ["vcf_known_indels_source"],
"vcf_known_indels_vcf_source": {
"meta": ["vcf_known_indels_vcf_source"],
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "Source of known_indels, cannot contain spaces"
Expand All @@ -306,8 +306,8 @@
"pattern": "^\\S+\\.vcf\\.gz\\.tbi?$",
"errorMessage": "VCF tabix index, cannot contain spaces"
},
"vcf_known_snps_source": {
"meta": ["vcf_known_snps_source"],
"vcf_known_snps_vcf_source": {
"meta": ["vcf_known_snps_vcf_source"],
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "Source of known_snps, cannot contain spaces"
Expand All @@ -324,8 +324,8 @@
"pattern": "^\\S+\\.vcf\\.gz\\.tbi?$",
"errorMessage": "VCF tabix index, cannot contain spaces"
},
"vcf_pon_source": {
"meta": ["vcf_pon_source"],
"vcf_pon_vcf_source": {
"meta": ["vcf_pon_vcf_source"],
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "Source of pon, cannot contain spaces"
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