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maxulysse merged 2 commits into from
Jul 16, 2020
Merged

better params handling #245

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ef52290
better params
maxulysse Jul 16, 2020
a1451dd
better params
maxulysse Jul 16, 2020
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135 changes: 64 additions & 71 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -178,55 +178,50 @@ if (tsv_path) {
*/

// Initialize each params in params.genomes, catch the command line first if it was defined
// params.fasta has to be the first one
params.fasta = params.genome && !('annotate' in step) ? params.genomes[params.genome].fasta ?: null : null

// The rest can be sorted
params.ac_loci = params.genome && 'ascat' in tools ? params.genomes[params.genome].ac_loci ?: null : null
params.ac_loci_gc = params.genome && 'ascat' in tools ? params.genomes[params.genome].ac_loci_gc ?: null : null
params.bwa = params.genome && params.fasta && 'mapping' in step ? params.genomes[params.genome].bwa ?: null : null
params.chr_dir = params.genome && 'controlfreec' in tools ? params.genomes[params.genome].chr_dir ?: null : null
params.chr_length = params.genome && 'controlfreec' in tools ? params.genomes[params.genome].chr_length ?: null : null
params.dbsnp = params.genome && ('mapping' in step || 'preparerecalibration' in step || 'controlfreec' in tools || 'haplotypecaller' in tools || 'mutect2' in tools || params.sentieon) ? params.genomes[params.genome].dbsnp ?: null : null
params.dbsnp_index = params.genome && params.dbsnp ? params.genomes[params.genome].dbsnp_index ?: null : null
params.dict = params.genome && params.fasta ? params.genomes[params.genome].dict ?: null : null
params.fasta_fai = params.genome && params.fasta ? params.genomes[params.genome].fasta_fai ?: null : null
params.germline_resource = params.genome && 'mutect2' in tools ? params.genomes[params.genome].germline_resource ?: null : null
params.germline_resource_index = params.genome && params.germline_resource ? params.genomes[params.genome].germline_resource_index ?: null : null
params.intervals = params.genome && !('annotate' in step) ? params.genomes[params.genome].intervals ?: null : null
params.known_indels = params.genome && ('mapping' in step || 'preparerecalibration' in step) ? params.genomes[params.genome].known_indels ?: null : null
params.known_indels_index = params.genome && params.known_indels ? params.genomes[params.genome].known_indels_index ?: null : null
params.mappability = params.genome && 'controlfreec' in tools ? params.genomes[params.genome].mappability ?: null : null
params.snpeff_db = params.genome && 'snpeff' in tools ? params.genomes[params.genome].snpeff_db ?: null : null
params.species = params.genome && 'vep' in tools ? params.genomes[params.genome].species ?: null : null
params.vep_cache_version = params.genome && 'vep' in tools ? params.genomes[params.genome].vep_cache_version ?: null : null

params.ac_loci = params.genome ? params.genomes[params.genome].ac_loci ?: false : false
params.ac_loci_gc = params.genome ? params.genomes[params.genome].ac_loci_gc ?: false : false
params.bwa = params.genome ? params.genomes[params.genome].bwa ?: false : false
params.chr_dir = params.genome ? params.genomes[params.genome].chr_dir ?: false : false
params.chr_length = params.genome ? params.genomes[params.genome].chr_length ?: false : false
params.dbsnp = params.genome ? params.genomes[params.genome].dbsnp ?: false : false
params.dbsnp_index = params.genome ? params.genomes[params.genome].dbsnp_index ?: false : false
params.dict = params.genome ? params.genomes[params.genome].dict ?: false : false
params.fasta = params.genome ? params.genomes[params.genome].fasta ?: false : false
params.fasta_fai = params.genome ? params.genomes[params.genome].fasta_fai ?: false : false
params.germline_resource = params.genome ? params.genomes[params.genome].germline_resource ?: false : false
params.germline_resource_index = params.genome ? params.genomes[params.genome].germline_resource_index ?: false : false
params.intervals = params.genome ? params.genomes[params.genome].intervals ?: false : false
params.known_indels = params.genome ? params.genomes[params.genome].known_indels ?: false : false
params.known_indels_index = params.genome ? params.genomes[params.genome].known_indels_index ?: false : false
params.mappability = params.genome ? params.genomes[params.genome].mappability ?: false : false
params.snpeff_db = params.genome ? params.genomes[params.genome].snpeff_db ?: false : false
params.species = params.genome ? params.genomes[params.genome].species ?: false : false
params.vep_cache_version = params.genome ? params.genomes[params.genome].vep_cache_version ?: false : false

// Initialize channels based on params
fasta = params.fasta && !('annotate' in step) ? Channel.value(file(params.fasta)) : "null"
dbsnp = params.dbsnp && ('mapping' in step || 'preparerecalibration' in step || 'controlfreec' in tools || 'haplotypecaller' in tools || 'mutect2' in tools || params.sentieon) ? Channel.value(file(params.dbsnp)) : "null"
germline_resource = params.germline_resource && 'mutect2' in tools ? Channel.value(file(params.germline_resource)) : "null"
known_indels = params.known_indels && ('mapping' in step || 'preparerecalibration' in step) ? Channel.value(file(params.known_indels)) : "null"
pon = params.pon ? Channel.value(file(params.pon)) : "null"

ch_ac_loci = params.ac_loci && 'ascat' in tools ? Channel.value(file(params.ac_loci)) : "null"
ch_ac_loci_gc = params.ac_loci_gc && 'ascat' in tools ? Channel.value(file(params.ac_loci_gc)) : "null"
ch_chr_dir = params.chr_dir && 'controlfreec' in tools ? Channel.value(file(params.chr_dir)) : "null"
ch_chr_length = params.chr_length && 'controlfreec' in tools ? Channel.value(file(params.chr_length)) : "null"
fai = params.fasta_fai && !('annotate' in step) ? Channel.value(file(params.fasta_fai)) : "null"
intervals = params.intervals && !params.no_intervals && !('annotate' in step) ? Channel.value(file(params.intervals)) : "null"
ch_mappability = params.mappability && 'controlfreec' in tools ? Channel.value(file(params.mappability)) : "null"

ch_snpeff_cache = params.snpeff_cache ? Channel.value(file(params.snpeff_cache)) : "null"
ch_snpeff_db = params.snpeff_db ? Channel.value(params.snpeff_db) : "null"
ch_vep_cache_version = params.vep_cache_version ? Channel.value(params.vep_cache_version) : "null"
ch_vep_cache = params.vep_cache ? Channel.value(file(params.vep_cache)) : "null"
chr_dir = params.chr_dir ?: Channel.empty()
chr_length = params.chr_length ?: Channel.empty()
dbsnp = params.dbsnp ?: Channel.empty()
fasta = params.fasta ?: Channel.empty()
germline_resource = params.germline_resource ?: Channel.empty()
known_indels = params.known_indels ?: Channel.empty()
loci = params.ac_loci ?: Channel.empty()
loci_gc = params.ac_loci_gc ?: Channel.empty()
mappability = params.mappability ?: Channel.empty()
pon = params.pon ?: Channel.empty()
snpeff_cache = params.snpeff_cache ?: Channel.empty()
snpeff_db = params.snpeff_db ?: Channel.empty()
snpeff_species = params.species ?: Channel.empty()
vep_cache = params.vep_cache ?: Channel.empty()
vep_cache_version = params.vep_cache_version ?: Channel.empty()

// Optional files, not defined within the params.genomes[params.genome] scope
ch_cadd_indels = params.cadd_indels ? Channel.value(file(params.cadd_indels)) : "null"
ch_cadd_indels_tbi = params.cadd_indels_tbi ? Channel.value(file(params.cadd_indels_tbi)) : "null"
ch_cadd_wg_snvs = params.cadd_wg_snvs ? Channel.value(file(params.cadd_wg_snvs)) : "null"
ch_cadd_wg_snvs_tbi = params.cadd_wg_snvs_tbi ? Channel.value(file(params.cadd_wg_snvs_tbi)) : "null"
ch_target_bed = params.target_bed ? Channel.value(file(params.target_bed)) : "null"
cadd_indels = params.cadd_indels ?: Channel.empty()
cadd_indels_tbi = params.cadd_indels_tbi ?: Channel.empty()
cadd_wg_snvs = params.cadd_wg_snvs ?: Channel.empty()
cadd_wg_snvs_tbi = params.cadd_wg_snvs_tbi ?: Channel.empty()
target_bed = params.target_bed ?: Channel.empty()

/*
================================================================================
Expand Down Expand Up @@ -322,8 +317,6 @@ include { MULTIQC } from './modules/nf-core/multiqc' params(params)

include { BUILD_INDICES } from './modules/subworkflows/build_indices' addParams(params)

fasta.dump(tag: 'fasta')

workflow {

BUILD_INDICES(
Expand All @@ -332,15 +325,17 @@ workflow {
germline_resource,
known_indels,
pon,
step)
step,
tools)

bwa = params.bwa ?: BUILD_INDICES.out.bwa
dbsnp_tbi = params.dbsnp ? params.dbsnp_index ?: BUILD_INDICES.out.dbsnp_tbi : Channel.empty()
dict = params.dict ?: BUILD_INDICES.out.dict
fai = params.fasta_fai ? params.fasta_fai : BUILD_INDICES.out.fai
germline_resource_tbi = params.germline_resource ? params.germline_resource_index ?: BUILD_INDICES.out.germline_resource_tbi : Channel.empty()
intervals = params.no_intervals ? Channel.empty() : params.intervals && !('annotate' in step) ? params.intervals : BUILD_INDICES.out.intervals
known_indels_tbi = params.known_indels ? params.known_indels_index ?: BUILD_INDICES.out.known_indels_tbi.collect() : Channel.empty()
intervals = params.no_intervals ? Channel.empty() : params.intervals ?: BUILD_INDICES.out.intervals
known_indels_tbi = params.known_indels ? params.known_indels_index ?: BUILD_INDICES.out.known_indels_tbi : Channel.empty()
// known_indels_tbi = params.known_indels ? params.known_indels_index ?: BUILD_INDICES.out.known_indels_tbi.collect() : Channel.empty()
pon_tbi = params.pon ? params.pon_index ?: BUILD_INDICES.out.pon_tbi : Channel.empty()

// PREPROCESSING
Expand Down Expand Up @@ -2292,7 +2287,7 @@ workflow.onComplete {

// input:
// set idPatient, idSample, file(bam), file(bai) from bamAscat
// file(acLoci) from ch_ac_loci
// file(acLoci) from loci
// file(dict) from dict
// file(fasta) from fasta
// file(fastaFai) from fai
Expand Down Expand Up @@ -2365,7 +2360,7 @@ workflow.onComplete {

// input:
// set idPatient, idSampleNormal, idSampleTumor, file(bafNormal), file(logrNormal), file(bafTumor), file(logrTumor) from convertAlleleCountsOut
// file(acLociGC) from ch_ac_loci_gc
// file(acLociGC) from loci_gc

// output:
// set val("ASCAT"), idPatient, idSampleNormal, idSampleTumor, file("${idSampleTumor}.*.{png,txt}") into ascatOut
Expand Down Expand Up @@ -2510,9 +2505,9 @@ workflow.onComplete {

// input:
// set idPatient, idSampleNormal, idSampleTumor, file(mpileupNormal), file(mpileupTumor) from mpileupOut
// file(chrDir) from ch_chr_dir
// file(mappability) from ch_mappability
// file(chrLength) from ch_chr_length
// file(chrDir) from chr_dir
// file(mappability) from mappability
// file(chrLength) from chr_length
// file(dbsnp) from dbsnp
// file(dbsnpIndex) from dbsnp_tbi
// file(fasta) from fasta
Expand Down Expand Up @@ -2801,8 +2796,8 @@ workflow.onComplete {

// input:
// set variantCaller, idSample, file(vcf) from vcfSnpeff
// file(dataDir) from ch_snpeff_cache
// val snpeffDb from ch_snpeff_db
// file(dataDir) from snpeff_cache
// val snpeffDb from snpeff_db

// output:
// set file("${reducedVCF}_snpEff.genes.txt"), file("${reducedVCF}_snpEff.html"), file("${reducedVCF}_snpEff.csv") into snpeffReport
Expand Down Expand Up @@ -2867,13 +2862,12 @@ workflow.onComplete {

// input:
// set variantCaller, idSample, file(vcf), file(idx) from vcfVep
// file(dataDir) from ch_vep_cache
// val cache_version from ch_vep_cache_version
// file(cadd_InDels) from ch_cadd_indels
// file(cadd_InDels_tbi) from ch_cadd_indels_tbi
// file(cadd_WG_SNVs) from ch_cadd_wg_snvs
// file(cadd_WG_SNVs_tbi) from ch_cadd_wg_snvs_tbi

// file(dataDir) from vep_cache
// val cache_version from vep_cache_version
// file(cadd_InDels) from cadd_indels
// file(cadd_InDels_tbi) from cadd_indels_tbi
// file(cadd_WG_SNVs) from cadd_wg_snvs
// file(cadd_WG_SNVs_tbi) from cadd_wg_snvs_tbi
// output:
// set variantCaller, idSample, file("${reducedVCF}_VEP.ann.vcf") into vepVCF
// file("${reducedVCF}_VEP.summary.html") into vepReport
Expand Down Expand Up @@ -2930,13 +2924,12 @@ workflow.onComplete {

// input:
// set variantCaller, idSample, file(vcf), file(idx) from compressVCFsnpEffOut
// file(dataDir) from ch_vep_cache
// val cache_version from ch_vep_cache_version
// file(cadd_InDels) from ch_cadd_indels
// file(cadd_InDels_tbi) from ch_cadd_indels_tbi
// file(cadd_WG_SNVs) from ch_cadd_wg_snvs
// file(cadd_WG_SNVs_tbi) from ch_cadd_wg_snvs_tbi

// file(dataDir) from vep_cache
// val cache_version from vep_cache_version
// file(cadd_InDels) from cadd_indels
// file(cadd_InDels_tbi) from cadd_indels_tbi
// file(cadd_WG_SNVs) from cadd_wg_snvs
// file(cadd_WG_SNVs_tbi) from cadd_wg_snvs_tbi
// output:
// set variantCaller, idSample, file("${reducedVCF}_VEP.ann.vcf") into vepVCFmerge
// file("${reducedVCF}_VEP.summary.html") into vepReportMerge
Expand Down
1 change: 1 addition & 0 deletions modules/subworkflows/build_indices.nf
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Expand Up @@ -25,6 +25,7 @@ workflow BUILD_INDICES{
known_indels
pon
step
tools
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